annotate backend/contrib/import_river.sh @ 7300:83bb52fa0c32

(issue1529) Be more tolerant in the fitting. The invalid value warning is removed because invalid data is expected there when datapoints are not valid for this KM
author Andre Heinecke <aheinecke@intevation.de>
date Fri, 11 Oct 2013 18:40:33 +0200
parents 14b5674e57a4
children 25912df0facf
rev   line source
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1 #!/bin/bash
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2 # Import script for rivers
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3 #
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4 # Authors:
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5 # Andre Heinecke <aheinecke@intevation.de>
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6 #
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7 # Copyright:
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8 # Copyright (C) 2013 Intevation GmbH
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9 #
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10 # This program is free software; you can redistribute it and/or
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11 # modify it under the terms of the GNU General Public License
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12 # as published by the Free Software Foundation; either version 2
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13 # of the License, or (at your option) any later version.
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14 #
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15 # This program is distributed in the hope that it will be useful,
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16 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 # GNU General Public License for more details.
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19 #
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20 # You should have received a copy of the GNU General Public License
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21 # along with this program; if not, write to the Free Software
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22 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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23
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24 set -e
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25
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26 # Default settings
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27 DEFAULT_HOST=localhost
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28 DEFAULT_PORT=1521
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29 DEFAULT_USER=flys_dami
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30 DEFAULT_PASS=flys_dami
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31 DEFAULT_LOG=$PWD/logs
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32 DEFAULT_BACKEND_NAME="XE"
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33 JAR="hydr_morph/importer.jar"
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34 IMPORTER_DRY_RUN=false
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35 IMPORTER_MAINVALUE_TYPES=QWTD
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36 IMPORTER_ANNOTATION_TYPES="conf/annotation-types.xml"
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37
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38
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39 MIN_MEMORY="8024m"
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40
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41 if [ -z "$OPTIONAL_LIBS" ]; then
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42 OPTIONAL_LIBS="$(dirname $0)/opt"
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43 fi
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44
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45 if [ -d "$OPTIONAL_LIBS" ]; then
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46 export PATH="$OPTIONAL_LIBS/bin:$PATH"
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47 export LD_LIBRARY_PATH="$OPTIONAL_LIBS/lib:$LD_LIBRARY_PATH"
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48 export LD_LIBRARY_PATH="$OPTIONAL_LIBS/lib64:$LD_LIBRARY_PATH"
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49 export PYTHONPATH="$OPTIONAL_LIBS/lib/python2.6/site-packages:$PYTHONPATH"
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50 export PYTHONPATH="$OPTIONAL_LIBS/lib64/python2.6/site-packages:$PYTHONPATH"
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51 export GDAL_DATA="$OPTIONAL_LIBS/share/gdal"
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52 fi
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53
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54 usage(){
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55 cat << EOF
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56
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57 usage: $0 [options] gew_file
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58
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59 Import a river described by the gew_file
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60
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61 OPTIONS:
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62 -?, --help Show this message
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63 -u, --username=<username> Database username. Default: $DEFAULT_USER
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64 -w, --password=<password> Database password. Default: $DEFAULT_PASS
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65 -h, --host=<host> Connect to database on host <host>.
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66 Default: $DEFAULT_HOST
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67 -p, --port=<number> Use port number <number>. Default: $DEFAULT_PORT
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68 -d, --db-name=<database_name> Name of the database / backend. Default: $DEFAULT_BACKEND_NAME
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69 -l, --log-dir=<directory> Directory in which to create the log files.
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70 Default: $LOG_DIR
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71 --postgres Database is PostgreSQL
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72 --skip-hydro Skip import of hydrological data
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73 --skip-morpho Skip import of morphological data
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74 --skip-geo Skip import of geographic data
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75 --skip-wst Skip import of wst data
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76 EOF
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77 exit 0
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78 }
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79
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80 OPTS=`getopt -o ?u:w:h:p:d: \
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81 -l help,username:,password:,host:,port:,db-name:,skip-hydro,skip-morpho,skip-geo,skip-wst,postgres \
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82 -n $0 -- "$@"`
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83 if [ $? != 0 ] ; then usage; fi
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84 eval set -- "$OPTS"
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85 while true ; do
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86 case "$1" in
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87 "-?"|"--help")
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88 usage;;
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89 "--")
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90 shift
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91 break;;
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92 "-u"|"--username")
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93 DBUSER=$2
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94 shift 2;;
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95 "-w"|"--password")
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96 DBPASS=$2
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97 shift 2;;
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98 "-h"|"--host")
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99 DBHOST=$2
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100 shift 2;;
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101 "-p"|"--port")
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102 DBPORT=$2
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103 shift 2;;
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104 "-l"|"--log-dir")
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105 LOG=$2
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106 shift 2;;
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107 "-d"|"--db-name")
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108 BACKEND_NAME=$2
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109 shift 2;;
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110 "--skip-hydro")
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111 SKIP_HYDRO="TRUE"
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112 shift;;
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113 "--skip-morpho")
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114 SKIP_MORPHO="TRUE"
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115 shift;;
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116 "--skip-wst")
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117 SKIP_WST="TRUE"
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118 shift;;
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119 "--skip-geo")
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120 SKIP_GEO="TRUE"
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121 shift;;
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122 "--postgres")
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123 POSTGRES="TRUE"
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124 shift;;
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125 *)
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126 echo "Unknown Option $1"
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127 usage;;
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128 esac
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129 done
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130
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131 if [ -z $DBUSER ]; then
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132 DBUSER=$DEFAULT_USER
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133 fi
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134 if [ -z $DBPASS ]; then
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135 DBPASS=$DEFAULT_PASS
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136 fi
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137 if [ -z $DBPORT ]; then
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138 DBPORT=$DEFAULT_PORT
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139 fi
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140 if [ -z $DBHOST ]; then
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141 DBHOST=$DEFAULT_HOST
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142 fi
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143 if [ -z $BACKEND_NAME ]; then
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144 BACKEND_NAME=$DEFAULT_BACKEND_NAME
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145 fi
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146 if [ -z $LOGDIR ]; then
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147 LOG=$DEFAULT_LOG
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148 fi
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149
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150 if [ $# != 1 ]; then
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parents:
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151 usage
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parents:
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152 fi
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153
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154 if [ ! -r $1 ]; then
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155 echo "Could not open $1 please ensure it exists and is readable"
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156 fi
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157
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158 GEW_FILE="$1"
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7c646d4d5103 be more flexible with river names (e.g. containing white space) in import script
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159 RIVER_NAME=$(grep "Gew.sser" "$1" | sed 's/Gew.sser: //')
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160 DATE=$(date +%Y.%m.%d_%H%M)
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161 LOG_DIR=${LOG}/`basename $GEW_FILE .gew`-$DATE
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162 mkdir -p ${LOG_DIR}
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163
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diff changeset
164 if [ "$POSTGRES" = "TRUE" ]; then
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165 JAR=$(echo "$JAR" | sed 's/importer/importer_psql/')
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166 if [ ! -r "$JAR" ]; then
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167 echo "Could not find Postgres importer $JAR"
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168 exit 1
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169 fi
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170 OGR_CONNECTION="PG:dbname=$BACKEND_NAME host=$DBHOST port=$DBPORT \
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171 user=$DBUSER password=$DBPASS"
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172 BACKEND_DB_PREFIX="jdbc:postgresql:"
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173 BACKEND_DB_DRIVER="org.postgresql.Driver"
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174 BACKEND_DB_DIALECT="org.hibernate.dialect.PostgreSQLDialect"
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diff changeset
175 else
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176 BACKEND_DB_PREFIX="jdbc:oracle:thin:@"
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177 BACKEND_DB_DRIVER="oracle.jdbc.OracleDriver"
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178 BACKEND_DB_DIALECT="org.hibernate.dialect.OracleDialect"
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179 fi
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180
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181 BACKEND_URL=$BACKEND_DB_PREFIX//$DBHOST:$DBPORT/$BACKEND_NAME
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182
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183 echo "Importing $RIVER_NAME into $BACKEND_URL."
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184
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185 import_hydro(){
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186 LOG_FILE=${LOG_DIR}/hydro.log
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187 echo Importing Hydrological data.
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188 echo Logging into: $LOG_FILE
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189 sed 's!./import.log!'"$LOG_FILE"'!' conf/log4j.properties > $LOG_DIR/log4j.properties
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diff changeset
190 java -jar \
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diff changeset
191 -Xmx$MIN_MEMORY \
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diff changeset
192 -server \
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193 -Dlog4j.configuration=file://$LOG_DIR/log4j.properties \
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diff changeset
194 -Dflys.backend.user=$DBUSER \
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195 -Dflys.backend.password=$DBPASS \
5167
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196 -Dflys.backend.url=$BACKEND_URL \
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diff changeset
197 -Dflys.backend.driver=$BACKEND_DB_DRIVER \
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diff changeset
198 -Dflys.backend.dialect=$BACKEND_DB_DIALECT \
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diff changeset
199 -Dflys.backend.importer.infogew.file="$GEW_FILE" \
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parents:
diff changeset
200 -Dflys.backend.main.value.types=$IMPORTER_MAINVALUE_TYPES \
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parents:
diff changeset
201 -Dflys.backend.importer.annotation.types=$IMPORTER_ANNOTATION_TYPES \
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diff changeset
202 -Dflys.backend.importer.dry.run=$IMPORTER_DRY_RUN \
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parents:
diff changeset
203 -Dflys.backend.importer.skip.annotations=false \
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parents:
diff changeset
204 -Dflys.backend.importer.skip.bwastr=false \
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parents:
diff changeset
205 -Dflys.backend.importer.skip.da50s=false \
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parents:
diff changeset
206 -Dflys.backend.importer.skip.da66s=false \
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parents:
diff changeset
207 -Dflys.backend.importer.skip.extra.wsts=false \
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parents:
diff changeset
208 -Dflys.backend.importer.skip.fixations=false \
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parents:
diff changeset
209 -Dflys.backend.importer.skip.flood.water=false \
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diff changeset
210 -Dflys.backend.importer.skip.flood.protection=false \
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diff changeset
211 -Dflys.backend.importer.skip.gauges=false \
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parents:
diff changeset
212 -Dflys.backend.importer.skip.historical.discharge.tables=false \
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parents:
diff changeset
213 -Dflys.backend.importer.skip.hyks=false \
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diff changeset
214 -Dflys.backend.importer.skip.official.lines=false \
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parents:
diff changeset
215 -Dflys.backend.importer.skip.prfs=false \
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diff changeset
216 -Dflys.backend.importer.skip.w80s=false \
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parents:
diff changeset
217 -Dflys.backend.importer.skip.wst=true \
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diff changeset
218 -Dflys.backend.importer.skip.measurement.stations=true \
5167
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219 -Dflys.backend.importer.skip.waterlevel.differences=true \
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parents:
diff changeset
220 -Dflys.backend.importer.skip.waterlevels=true \
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parents:
diff changeset
221 -Dflys.backend.importer.skip.sq.relation=true \
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parents:
diff changeset
222 -Dflys.backend.importer.skip.sediment.density=true \
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parents:
diff changeset
223 -Dflys.backend.importer.skip.sediment.yield=true \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
224 -Dflys.backend.importer.skip.morphological.width=true \
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parents:
diff changeset
225 -Dflys.backend.importer.skip.flow.velocity=true \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
226 -Dflys.backend.importer.skip.bed.height.single=true \
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parents:
diff changeset
227 -Dflys.backend.importer.skip.bed.height.epoch=true \
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parents:
diff changeset
228 $JAR
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parents:
diff changeset
229 }
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parents:
diff changeset
230
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parents:
diff changeset
231 import_morpho(){
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diff changeset
232 LOG_FILE=${LOG_DIR}/morpho.log
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parents:
diff changeset
233 echo Importing Morphological data.
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parents:
diff changeset
234 echo Logging into: $LOG_FILE
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parents:
diff changeset
235 sed 's!./import.log!'"$LOG_FILE"'!' conf/log4j.properties > $LOG_DIR/log4j.properties
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parents:
diff changeset
236 java -jar \
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parents:
diff changeset
237 -Xmx$MIN_MEMORY \
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parents:
diff changeset
238 -server \
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parents:
diff changeset
239 -Dlog4j.configuration=file://$LOG_DIR/log4j.properties \
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diff changeset
240 -Dflys.backend.user=$DBUSER \
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parents: 5176
diff changeset
241 -Dflys.backend.password=$DBPASS \
5167
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parents:
diff changeset
242 -Dflys.backend.url=$BACKEND_URL \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
243 -Dflys.backend.driver=$BACKEND_DB_DRIVER \
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parents:
diff changeset
244 -Dflys.backend.dialect=$BACKEND_DB_DIALECT \
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parents:
diff changeset
245 -Dflys.backend.importer.infogew.file="$GEW_FILE" \
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parents:
diff changeset
246 -Dflys.backend.main.value.types=$IMPORTER_MAINVALUE_TYPES \
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parents:
diff changeset
247 -Dflys.backend.importer.annotation.types=$IMPORTER_ANNOTATION_TYPES \
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parents:
diff changeset
248 -Dflys.backend.importer.dry.run=$IMPORTER_DRY_RUN \
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parents:
diff changeset
249 -Dflys.backend.importer.skip.annotations=true \
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parents:
diff changeset
250 -Dflys.backend.importer.skip.bwastr=true \
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parents:
diff changeset
251 -Dflys.backend.importer.skip.da50s=true \
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parents:
diff changeset
252 -Dflys.backend.importer.skip.da66s=true \
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parents:
diff changeset
253 -Dflys.backend.importer.skip.extra.wsts=true \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
254 -Dflys.backend.importer.skip.fixations=true \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
255 -Dflys.backend.importer.skip.flood.water=true \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
256 -Dflys.backend.importer.skip.flood.protection=true \
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parents:
diff changeset
257 -Dflys.backend.importer.skip.gauges=true \
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parents:
diff changeset
258 -Dflys.backend.importer.skip.historical.discharge.tables=true \
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parents:
diff changeset
259 -Dflys.backend.importer.skip.hyks=true \
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parents:
diff changeset
260 -Dflys.backend.importer.skip.official.lines=true \
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parents:
diff changeset
261 -Dflys.backend.importer.skip.prfs=true \
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parents:
diff changeset
262 -Dflys.backend.importer.skip.w80s=true \
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parents:
diff changeset
263 -Dflys.backend.importer.skip.wst=true \
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parents: 5838
diff changeset
264 -Dflys.backend.importer.skip.measurement.stations=false \
5167
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diff changeset
265 -Dflys.backend.importer.skip.waterlevel.differences=false \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
266 -Dflys.backend.importer.skip.waterlevels=false \
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Andre Heinecke <aheinecke@intevation.de>
parents:
diff changeset
267 -Dflys.backend.importer.skip.sq.relation=false \
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parents:
diff changeset
268 -Dflys.backend.importer.skip.sediment.density=false \
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parents:
diff changeset
269 -Dflys.backend.importer.skip.sediment.yield=false \
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parents:
diff changeset
270 -Dflys.backend.importer.skip.morphological.width=false \
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parents:
diff changeset
271 -Dflys.backend.importer.skip.flow.velocity=false \
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parents:
diff changeset
272 -Dflys.backend.importer.skip.bed.height.single=false \
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parents:
diff changeset
273 -Dflys.backend.importer.skip.bed.height.epoch=false \
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parents:
diff changeset
274 $JAR
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parents:
diff changeset
275 }
a0abb6787ab1 Add first version of import_river script
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parents:
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276
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277 import_wst(){
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278 LOG_FILE=${LOG_DIR}/wst.log
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279 echo Importing WST data.
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280 echo Logging into: $LOG_FILE
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281 sed 's!./import.log!'"$LOG_FILE"'!' conf/log4j.properties > $LOG_DIR/log4j.properties
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282 java -jar \
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283 -Xmx$MIN_MEMORY \
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284 -server \
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285 -Dlog4j.configuration=file://$LOG_DIR/log4j.properties \
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286 -Dflys.backend.user=$DBUSER \
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287 -Dflys.backend.password=$DBPASS \
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288 -Dflys.backend.url=$BACKEND_URL \
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289 -Dflys.backend.driver=$BACKEND_DB_DRIVER \
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290 -Dflys.backend.dialect=$BACKEND_DB_DIALECT \
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291 -Dflys.backend.importer.infogew.file="$GEW_FILE" \
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292 -Dflys.backend.main.value.types=$IMPORTER_MAINVALUE_TYPES \
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293 -Dflys.backend.importer.annotation.types=$IMPORTER_ANNOTATION_TYPES \
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294 -Dflys.backend.importer.dry.run=$IMPORTER_DRY_RUN \
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295 -Dflys.backend.importer.skip.annotations=true \
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296 -Dflys.backend.importer.skip.bwastr=true \
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297 -Dflys.backend.importer.skip.da50s=true \
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298 -Dflys.backend.importer.skip.da66s=true \
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299 -Dflys.backend.importer.skip.extra.wsts=true \
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300 -Dflys.backend.importer.skip.fixations=true \
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301 -Dflys.backend.importer.skip.flood.water=true \
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302 -Dflys.backend.importer.skip.flood.protection=true \
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303 -Dflys.backend.importer.skip.gauges=true \
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304 -Dflys.backend.importer.skip.historical.discharge.tables=true \
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305 -Dflys.backend.importer.skip.hyks=true \
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306 -Dflys.backend.importer.skip.official.lines=true \
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307 -Dflys.backend.importer.skip.prfs=true \
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308 -Dflys.backend.importer.skip.w80s=true \
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309 -Dflys.backend.importer.skip.wst=false \
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310 -Dflys.backend.importer.skip.measurement.stations=true \
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311 -Dflys.backend.importer.skip.waterlevel.differences=true \
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312 -Dflys.backend.importer.skip.waterlevels=true \
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313 -Dflys.backend.importer.skip.sq.relation=true \
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314 -Dflys.backend.importer.skip.sediment.density=true \
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315 -Dflys.backend.importer.skip.sediment.yield=true \
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316 -Dflys.backend.importer.skip.morphological.width=true \
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317 -Dflys.backend.importer.skip.flow.velocity=true \
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318 -Dflys.backend.importer.skip.bed.height.single=true \
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319 -Dflys.backend.importer.skip.bed.height.epoch=true \
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320 $JAR
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321 }
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322
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323 import_geo(){
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324 LOG_FILE=${LOG_DIR}/geo.log
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325 echo Importing Geographic data.
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326 echo Logging into: $LOG_FILE
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327
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328 RIVER_PATH=$(grep "WSTDatei:" "$GEW_FILE" | awk '{print $2}')
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329 RIVER_PATH=$(dirname "$RIVER_PATH")/../..
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330 RIVER_PATH=$(readlink -f "$RIVER_PATH")
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331
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332 exec python $(dirname $0)/geodaesie/shpimporter.py \
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333 --directory $RIVER_PATH \
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334 --river_name "$RIVER_NAME" \
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335 --ogr_connection "$OGR_CONNECTION" \
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336 --host $DBHOST \
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337 --user $DBUSER \
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338 --password $DBPASS \
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339 --verbose 1 \
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340 > "$LOG_FILE" 2>&1
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341 }
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342
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343
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344 if [ "$SKIP_HYDRO" != "TRUE" ]; then
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345 import_hydro
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346 fi
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347 if [ "$SKIP_WST" != "TRUE" ]; then
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348 import_wst
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349 fi
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350 if [ "$SKIP_MORPHO" != "TRUE" ]; then
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351 import_morpho
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352 fi
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353 if [ "$SKIP_GEO" != "TRUE" ]; then
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354 import_geo
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355 fi

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