1 <?xml version="1.0" encoding="UTF-8"?>
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3 <project default="build-server" name="compbio-ws" basedir=".">
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6 <property name="classes" location="${basedir}/WEB-INF/classes" />
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7 <property name="lib.path" location="${basedir}/WEB-INF/lib" />
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9 <path id="classes.path">
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10 <pathelement location="${classes}" />
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13 <!-- add libraries -->
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14 <path id="project.classpath">
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15 <fileset dir="${lib.path}">
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16 <include name="*.jar" />
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20 <property name="wsdl.dir" location="${basedir}/webservices/compbio/ws/server/resource" />
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21 <property name="jpred.wsdl" location="${wsdl.dir}/JpredWS.wsdl" />
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22 <property name="aacon.wsdl" location="${wsdl.dir}/AAConWS.wsdl" />
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23 <property name="clustal.wsdl" location="${wsdl.dir}/ClustalWS.wsdl" />
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24 <property name="muscle.wsdl" location="${wsdl.dir}/MuscleWS.wsdl" />
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25 <property name="tcoffee.wsdl" location="${wsdl.dir}/TcoffeeWS.wsdl" />
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26 <property name="mafft.wsdl" location="${wsdl.dir}/MafftWS.wsdl" />
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27 <property name="glprobs.wsdl" location="${wsdl.dir}/GLprobsWS.wsdl" />
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28 <property name="msaprobs.wsdl" location="${wsdl.dir}/MSAprobsWS.wsdl" />
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30 <property name="disembl.wsdl" location="${wsdl.dir}/DisemblWS.wsdl" />
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31 <property name="globplot.wsdl" location="${wsdl.dir}/GlobPlotWS.wsdl" />
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32 <property name="iupred.wsdl" location="${wsdl.dir}/IUPredWS.wsdl" />
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33 <property name="jronn.wsdl" location="${wsdl.dir}/JronnWS.wsdl" />
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35 <property name="registry.wsdl" location="${wsdl.dir}/RegistryWS.wsdl" />
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36 <property name="rnaalifold.wsdl" location="${wsdl.dir}/RNAalifold.wsdl" />
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38 <taskdef name="wsgen" onerror="report" classname="com.sun.tools.ws.ant.WsGen">
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39 <classpath refid="project.classpath" />
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42 <target name="build-server">
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43 <!-- TODO this runs file from Eclipse, but with Ant only this need to depends on clean and build! -->
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44 <property name="server.artifacts.dir" location="${basedir}/webservices/compbio/ws/server/jaxws/" />
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46 <mkdir dir="${server.artifacts.dir}" />
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47 <mkdir dir="${wsdl.dir}" />
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48 <delete quiet="false" verbose="true" failonerror="false">
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49 <fileset dir="${server.artifacts.dir}">
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50 <include name="*.java" />
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52 <fileset dir="${wsdl.dir}">
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56 <!-- destdir - Where to put generated classes -->
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57 <!-- sourcedestdir - Where to put generated source files -->
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58 <!-- resourcedestdir - Where to put generated source files -->
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59 <wsgen sei="compbio.ws.server.JpredWS"
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60 sourcedestdir="${basedir}/webservices"
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61 destdir="${classes}"
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62 resourcedestdir="${wsdl.dir}"
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68 <classpath refid="classes.path" />
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69 <classpath refid="project.classpath" />
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71 <wsgen sei="compbio.ws.server.AAConWS"
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72 sourcedestdir="${basedir}/webservices"
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73 destdir="${classes}"
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74 resourcedestdir="${wsdl.dir}"
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80 <classpath refid="classes.path" />
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81 <classpath refid="project.classpath" />
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83 <wsgen sei="compbio.ws.server.MSAprobsWS"
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84 sourcedestdir="${basedir}/webservices"
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85 destdir="${classes}"
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86 resourcedestdir="${wsdl.dir}"
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92 <classpath refid="classes.path" />
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93 <classpath refid="project.classpath" />
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95 <wsgen sei="compbio.ws.server.GLprobsWS"
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96 sourcedestdir="${basedir}/webservices"
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97 destdir="${classes}"
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98 resourcedestdir="${wsdl.dir}"
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104 <classpath refid="classes.path" />
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105 <classpath refid="project.classpath" />
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107 <wsgen sei="compbio.ws.server.ClustalWS"
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108 sourcedestdir="${basedir}/webservices"
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109 destdir="${classes}"
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110 resourcedestdir="${wsdl.dir}"
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116 <classpath refid="classes.path" />
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117 <classpath refid="project.classpath" />
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119 <wsgen sei="compbio.ws.server.MuscleWS"
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120 sourcedestdir="${basedir}/webservices"
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121 destdir="${classes}"
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122 resourcedestdir="${wsdl.dir}"
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128 <classpath refid="classes.path" />
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129 <classpath refid="project.classpath" />
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131 <wsgen sei="compbio.ws.server.MafftWS"
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132 sourcedestdir="${basedir}/webservices"
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133 destdir="${classes}"
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134 resourcedestdir="${wsdl.dir}"
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140 <classpath refid="classes.path" />
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141 <classpath refid="project.classpath" />
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143 <wsgen sei="compbio.ws.server.TcoffeeWS"
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144 sourcedestdir="${basedir}/webservices"
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145 destdir="${classes}"
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146 resourcedestdir="${wsdl.dir}"
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152 <classpath refid="classes.path" />
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153 <classpath refid="project.classpath" />
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155 <wsgen sei="compbio.ws.server.DisemblWS"
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156 sourcedestdir="${basedir}/webservices"
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157 destdir="${classes}"
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158 resourcedestdir="${wsdl.dir}"
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164 <classpath refid="classes.path" />
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165 <classpath refid="project.classpath" />
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167 <wsgen sei="compbio.ws.server.GlobPlotWS"
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168 sourcedestdir="${basedir}/webservices"
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169 destdir="${classes}"
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170 resourcedestdir="${wsdl.dir}"
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176 <classpath refid="classes.path" />
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177 <classpath refid="project.classpath" />
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179 <wsgen sei="compbio.ws.server.JronnWS"
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180 sourcedestdir="${basedir}/webservices"
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181 destdir="${classes}"
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182 resourcedestdir="${wsdl.dir}"
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188 <classpath refid="classes.path" />
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189 <classpath refid="project.classpath" />
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191 <wsgen sei="compbio.ws.server.IUPredWS"
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192 sourcedestdir="${basedir}/webservices"
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193 destdir="${classes}"
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194 resourcedestdir="${wsdl.dir}"
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200 <classpath refid="classes.path" />
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201 <classpath refid="project.classpath" />
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203 <wsgen sei="compbio.ws.server.RegistryWS"
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204 sourcedestdir="${basedir}/webservices"
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205 destdir="${classes}"
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206 resourcedestdir="${wsdl.dir}"
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212 <classpath refid="classes.path" />
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213 <classpath refid="project.classpath" />
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215 <wsgen sei="compbio.ws.server.RNAalifoldWS"
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216 sourcedestdir="${basedir}/webservices"
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217 destdir="${classes}"
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218 resourcedestdir="${wsdl.dir}"
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219 keep="true" genwsdl="true"
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223 <classpath refid="classes.path" />
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224 <classpath refid="project.classpath" />
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228 <taskdef name="wsimport" classname="com.sun.tools.ws.ant.WsImport">
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229 <classpath refid="project.classpath" />
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232 <target name="build-clients">
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233 <property name="client.artifacts.dir" location="${basedir}/webservices/compbio/ws/client/stub" />
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235 <mkdir dir="${client.artifacts.dir}" />
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236 <delete quiet="false" verbose="true" failonerror="true">
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237 <fileset dir="${client.artifacts.dir}">
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238 <include name="*.java" />
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242 <wsimport wsdl="${clustal.wsdl}"
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243 sourcedestdir="${basedir}/webservices/"
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244 keep="true" extension="false"
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245 verbose="true" xnocompile="true" xendorsed="true"
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246 package="compbio.ws.client.stub" target="2.1"
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250 <wsimport wsdl="${muscle.wsdl}"
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251 sourcedestdir="${basedir}/webservices/"
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252 keep="true" extension="false"
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253 verbose="true" xnocompile="true" xendorsed="true"
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254 package="compbio.ws.client.stub" target="2.1"
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258 <wsimport wsdl="${mafft.wsdl}"
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259 sourcedestdir="${basedir}/webservices/"
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260 keep="true" extension="false"
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261 verbose="true" xnocompile="true" xendorsed="true"
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262 package="compbio.ws.client.stub" target="2.1"
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266 <wsimport wsdl="${tcoffee.wsdl}"
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267 sourcedestdir="${basedir}/webservices/"
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268 keep="true" extension="false"
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269 verbose="true" xnocompile="true" xendorsed="true"
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270 package="compbio.ws.client.stub" target="2.1"
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274 <wsimport wsdl="${iupred.wsdl}"
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275 sourcedestdir="${basedir}/webservices/"
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276 keep="true" extension="false"
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277 verbose="true" xnocompile="true" xendorsed="true"
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278 package="compbio.ws.client.stub" target="2.1"
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282 <wsimport wsdl="${registry.wsdl}"
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283 sourcedestdir="${basedir}/webservices/"
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284 keep="true" extension="false"
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285 verbose="true" xnocompile="true" xendorsed="true"
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286 package="compbio.ws.client.stub" target="2.1"
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290 <wsimport wsdl="${rnaalifold.wsdl}"
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291 sourcedestdir="${basedir}/webservices/"
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292 keep="true" extension="false"
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293 verbose="true" xnocompile="true" xendorsed="true"
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294 package="compbio.ws.client.stub" target="2.1"
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301 <target name="Build artifacts from schema" description="Test task to generate JaxB commons annotated data classes DOES NOT REALLY WORK">
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302 <taskdef name="xjc" classname="com.sun.tools.xjc.XJCTask">
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303 <classpath refid="project.classpath" />
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305 <mkdir dir="${basedir}/src/test" />
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306 <xjc schema="${wsdl.dir}/SyncMsaWS_schema1.xsd" destdir="${basedir}/src/test">
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307 <arg value="-Xcommons-lang" />
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309 <produces dir="${basedir}/src/test" />
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310 <classpath refid="classes.path" />
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312 <fileset dir="${basedir}/lib">
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313 //JAXB2 Basics library
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314 <include name="jaxb2-basics-*.jar"/>
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315 // JAXB2 Basics library dependencies
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316 <include name="jaxb2-basics-runtime-*.jar"/>
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317 <include name="jaxb2-basics-tools-*.jar"/>
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318 <include name="commons-beanutils-*.jar"/>
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319 <include name="commons-lang-*.jar"/>
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320 <include name="commons-logging-*.jar"/>
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331 <target name="build-Clustal-client-from-live-server">
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333 <wsimport wsdl="http://localhost:7979/ClustalWS?wsdl"
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334 sourcedestdir="${basedir}/webservices/"
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339 package="compbio.ws.client.stub"
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344 <target name="build-Muscle-client-from-live-server">
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345 <wsimport wsdl="http://localhost:7979/MuscleWS?wsdl"
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346 sourcedestdir="${basedir}/webservices/"
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351 package="compbio.ws.client.stub"
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357 <target name="build-client-jar" description="Pack WS client into a single jar THIS IS EXAMPLE ONLY!">
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358 <echo>Jar file: wsclient</echo>
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359 <delete file="${basedir}/resources/wsclient.jar">
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361 <jar jarfile="${basedir}/resources/wsclient.jar">
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362 <fileset dir="${basedir}/WebContent/WEB-INF/classes/" includes="org/pimslims/ws/client/**/*.class" />
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363 <fileset dir="${classes}" includes="org/pimslims/sec/*,org/pimslims/lab/Util.class" />
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364 <zipfileset excludes="META-INF/*.SF" src="D:/workspace/current-pims-web/WebContent/WEB-INF/lib/webservices-rt.jar" />
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366 <attribute name="Built-By" value="${user.name}" />
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367 <attribute name="Main-Class" value="org.pimslims.ws.client.FileUploadClient" />
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368 <attribute name="Class-Path" value="." />
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369 <attribute name="Implementation-Title" value="PIMS File Upload Web Service Client" />
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370 <attribute name="Implementation-Vendor" value="The PIMS team" />
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371 <attribute name="Implementation-URL" value="http://www.pims-lims.org" />
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377 <target name="run-client-jar" description="THIS IS EXAMPLE ONLY">
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378 <java jar="${basedir}/resources/wsclient.jar" fork="true" failonerror="true" maxmemory="256m">
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379 <arg value="C:/Documents and Settings/pvt43/Desktop/Leeds Sequencing/Copy of Files to up load" />
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383 <target name="run-client-class" description="THIS IS EXAMPLE ONLY">
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384 <java classname="org.pimslims.ws.client.FileUploadClient" fork="true" failonerror="true" maxmemory="256m">
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385 <classpath refid="project.classpath" />
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386 <classpath refid="instrument.classpath" />
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