build.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2
   3 <project default="build-all" name="Build Java Bioinformatics Analysis Web Services" basedir=".">
   4
   5         <property name="LD_LIBRARY_PATH" value="/gridware/sge/lib/lx24-amd64"/>
   6
   7         <!-- Distributive file names-->
   8         <property name="distdir" value="website/archive"/>
   9         <mkdir dir="${distdir}" />
  10
  11         <!-- projects details -->
  12         <property name="project.url" value="http://www.compbio.dundee.ac.uk/jabaws"/>
  13         <property name="product" value="Java Bioinformatics Analyses Web Services"/>
  14         <property name="author" value="Alexander Sherstnev, Peter Troshin"/>
  15
  16         <!-- dependencies on other compbio projects  -->
  17         <property name="compbio-annotation" value="compbio-annotations-1.0.jar"/>
  18         <property name="compbio-util" value="compbio-util-1.4.jar"/>
  19         <property name="compbio-ga" value="compbio-ga-1.1.jar"/>
  20
  21         <!-- products -->
  22         <property name="jabaws_version" value="2.1.0"/>
  23         <property name="core" value="${distdir}/jabaws-core-${jabaws_version}.jar"/>
  24         <property name="core-src" value="${distdir}/jabaws-core-src-${jabaws_version}.jar"/>
  25         <property name="datamodel" value="${distdir}/datamodel-${jabaws_version}.jar"/>
  26         <property name="datamodel-src" value="${distdir}/datamodel-src-${jabaws_version}.jar"/>
  27         <property name="min-jabaws-client" value="${distdir}/min-jabaws-client-${jabaws_version}.jar"/>
  28         <property name="stat-updater" value="${distdir}/stat-updater-${jabaws_version}.jar"/>
  29         <property name="min-jabaws-client-nolog" value="${distdir}/min-jabaws-client-nolog-${jabaws_version}.jar"/>
  30         <property name="jabaws-client-src" value="${distdir}/jabaws-client-src-${jabaws_version}.jar"/>
  31         <property name="full-jabaws-client" value="${distdir}/full-jabaws-client-${jabaws_version}.jar"/>
  32         <property name="jabaws-source-jar" value="${distdir}/jabaws-src-${jabaws_version}.jar"/>
  33         <property name="full-jabaws-client-pack" value="${distdir}/full-jabaws-client-${jabaws_version}-pack.zip"/>
  34         <property name="jabaws" value="${distdir}/jabaws.war"/>
  35         <property name="jabaws-no-binaries" value="${distdir}/jabaws-no-binaries.war"/>
  36         <property name="binaries" value="${distdir}/binaries.zip"/>
  37         <property name="jabaws-devel-web" value="${distdir}/jabaws-devel-website.zip"/>
  38
  39         <!--Whole project archive -->
  40         <property name="jabaws-project" value="${distdir}/jabaws-project.zip"/>
  41
  42         <!-- java -->
  43         <property name="test.src" location="${basedir}/testsrc" />
  44         <property name="classes" location="${basedir}/WEB-INF/classes" />
  45         <property name="lib.path" location="${basedir}/lib" />
  46         <property name="web.lib.path" location="${basedir}/WEB-INF/lib" />
  47         <property name="test.lib.path" location="${basedir}/testsrc/lib" />
  48         <property name="activity.log" location="${basedir}/activity.log" />
  49
  50         <!-- add libraries -->
  51         <path id="project.classpath">
  52                 <fileset dir="${lib.path}">
  53                         <include name="*.jar" />
  54                 </fileset>
  55                 <fileset dir="${web.lib.path}">
  56                         <include name="*.jar" />
  57                 </fileset>
  58         </path>
  59
  60         <!-- add test classes -->
  61         <path id="test.classpath">
  62                 <fileset dir="${test.lib.path}">
  63                         <include name="*.jar" />
  64                 </fileset>
  65                 <pathelement location="${classes}" />
  66         </path>
  67
  68         <fileset dir="${basedir}/WEB-INF/classes/" id="fullclient">
  69                 <!-- Datamodel -->
  70                 <include name="compbio/data/**"/>
  71                 <include name="compbio/metadata/**"/>
  72                 <!-- Engines -->
  73                 <include name="compbio/engine/**"/>
  74                 <!-- Runners -->
  75                 <include name="compbio/runner/**"/>
  76                 <!-- Logging configuration -->
  77         </fileset>
  78
  79         <fileset dir="${basedir}/WEB-INF/classes/" id="statupdater">
  80                 <!-- Datamodel -->
  81                 <include name="compbio/data/**"/>
  82                 <include name="compbio/metadata/**"/>
  83                 <!-- Engines -->
  84                 <include name="compbio/engine/**"/>
  85                 <!-- Runners -->
  86                 <include name="compbio/runner/**"/>
  87                 <!-- Runners -->
  88                 <include name="compbio/stat/collector/**"/>
  89                 <include name="compbio/ws/client/**"/>
  90                 <!-- Logging configuration -->
  91         </fileset>
  92
  93
  94
  95         <!-- Clean temp directories -->
  96         <target name="clean">
  97                 <delete dir="${classes}" />
  98                 <delete dir="${basedir}/logs" />
  99                 <delete file="${distdir}/binaries.zip" />
 100                 <delete file="${basedir}/activity.log" />
 101                 <delete file="${basedir}/derby.log" />
 102                 <mkdir dir="${classes}" />
 103                 <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
 104         </target>
 105
 106         <!-- Clean up temp directories and dist directory (all jar, zip, and war files deleted) -->
 107         <target name="full-clean" depends="clean">
 108                 <delete>
 109                         <fileset dir="${distdir}">
 110                                 <include name="*.jar"/>
 111                                 <include name="*.zip"/>
 112                                 <include name="*.war"/>
 113                         </fileset>
 114                 </delete>
 115         </target>
 116
 117         <target name="clearStatDB" description="Remove all records from statistics database">
 118                 <echo>Cleaning Statistics database</echo>
 119                 <java classname="compbio.stat.collector.StatDB" fork="true" failonerror="true" classpath="${classes}">
 120                         <jvmarg value="-Dlog4j.configuration=file:log/log4j.properties.statdb" />
 121                         <classpath refid="project.classpath" />
 122                 </java>
 123         </target>
 124
 125         <!--
 126         The compilation order is
 127         1. datamodel
 128         2. engine
 129         3. runner
 130         4. testscr
 131         5. webservices
 132         Packages of the lower order could not have dependencies on the packages on the next layer.
 133         So runners (layer 3) depends on the engines and the datamodel but engines does not depend on
 134         anything in runners or any other layers above. Testsrc is not allowed to test webservices.
 135         -->
 136         <target name="compile_with_debug" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug enabled.">
 137                 <!-- copy files to class path-->
 138                 <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
 139                 <!-- Complile the datamodel first -->
 140                 <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 141                         <compilerarg value="-Xlint:unchecked"/>
 142                         <classpath refid="project.classpath" />
 143                 </javac>
 144                 <!-- Complile the engines -->
 145                 <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 146                         <compilerarg value="-Xlint:unchecked"/>
 147                         <classpath refid="project.classpath" />
 148                 </javac>
 149                 <!-- Complile the runners -->
 150                 <javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 151                         <compilerarg value="-Xlint:unchecked"/>
 152                         <classpath refid="project.classpath" />
 153                 </javac>
 154                 <!-- Complile the webservices -->
 155                 <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 156                         <compilerarg value="-Xlint:unchecked"/>
 157                         <classpath refid="project.classpath" />
 158                 </javac>
 159                 <!-- Complile the tests -->
 160                 <javac srcdir="${basedir}/testsrc" destdir="${classes}" target="1.6" debug="on" encoding="UTF-8" verbose="false" nowarn="true" >
 161                         <compilerarg value="-Xlint:unchecked"/>
 162                         <classpath refid="project.classpath" />
 163                         <classpath refid="test.classpath" />
 164                 </javac>
 165         </target>
 166
 167         <!--
 168         Compile with optimisation. Do not compile testsrc
 169         The compilation order is
 170         1. datamodel
 171         2. engine
 172         3. runner
 173         4. webservices
 174         Packages of the lower order could not have dependencies on the packages on the next layer.
 175         So runners (layer 3) depends on the engines and the datamodel but engines does not depend
 176         on anything in runners or any other layers above.
 177         -->
 178         <target name="compile" depends="clean" description="Perform a multiple step compilation to ensure layered structure is preserved. Debug disabled, optimisation enabled. Tests are not compiled.">
 179                 <!-- copy files to class path-->
 180                 <copy file="${basedir}/log/log4j.properties" tofile="${classes}/log4j.properties" />
 181                 <!-- Complile the datamodel first -->
 182                 <javac srcdir="${basedir}/datamodel" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 183                         <compilerarg value="-Xlint:-unchecked" />
 184                         <classpath refid="project.classpath" />
 185                 </javac>
 186                 <!-- Complile the engines -->
 187                 <javac srcdir="${basedir}/engine" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 188                         <compilerarg value="-Xlint:all" />
 189                         <compilerarg value="-Xlint:-unchecked" />
 190                         <classpath refid="project.classpath" />
 191                 </javac>
 192                 <!-- Complile the runners -->
 193                 <javac srcdir="${basedir}/runner" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 194                         <compilerarg value="-Xlint:-unchecked" />
 195                         <classpath refid="project.classpath" />
 196                 </javac>
 197                 <!-- Complile the webservices -->
 198                 <javac srcdir="${basedir}/webservices" destdir="${classes}" target="1.6" source="1.6" includeantruntime="false" debug="off" optimize="on" encoding="UTF-8" verbose="false" nowarn="true">
 199                         <compilerarg value="-Xlint:-unchecked" />
 200                         <classpath refid="project.classpath" />
 201                 </javac>
 202         </target>
 203
 204         <target name="datamodel-jar" depends="compile" description="Pack data model classes">
 205                 <echo>Jar file: Minimal WS client jar</echo>
 206                 <delete file="${basedir}/${datamodel}"></delete>
 207                 <jar jarfile="${basedir}/${datamodel}">
 208                         <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 209                                 <include name="${compbio-util}"/>
 210                                 <include name="${compbio-annotation}"/>
 211                         </zipgroupfileset>
 212                         <fileset dir="${basedir}/WEB-INF/classes/">
 213                                 <include name="compbio/data/sequence/*.class"/>
 214                                 <include name="compbio/metadata/*.class"/>
 215                         </fileset>
 216                         <manifest>
 217                                 <attribute name="Built-By" value="${author}" />
 218                                 <attribute name="Class-Path" value="." />
 219                                 <attribute name="Implementation-Title" value="Datamodel for ${product} " />
 220                                 <attribute name="Implementation-Vendor" value="${author}" />
 221                                 <attribute name="Implementation-URL" value="${project.url}" />
 222                         </manifest>
 223                 </jar>
 224         </target>
 225
 226         <target name="datamodel-source-jar" depends="compile" description="Pack java sources">
 227                 <delete file="${datamodel-src}"></delete>
 228                 <jar jarfile="${datamodel-src}">
 229                         <fileset dir="${basedir}/datamodel">
 230                                 <include name="**"/>
 231                         </fileset>
 232                         <zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
 233                                 <include name="**"/>
 234                         </zipgroupfileset>
 235                         <manifest>
 236                                 <attribute name="Built-By" value="${author}" />
 237                                 <attribute name="Implementation-Title" value="${product} Datamodel Source Code Archive" />
 238                                 <attribute name="Implementation-Vendor" value="${author}" />
 239                                 <attribute name="Implementation-URL" value="${project.url}" />
 240                         </manifest>
 241                 </jar>
 242         </target>
 243
 244         <target name="core-jar" depends="compile" description="Pack jabaws core classes">
 245                 <echo>Jar file: JABAWS core jar</echo>
 246                 <delete file="${basedir}/${core}"></delete>
 247                 <jar jarfile="${basedir}/${core}">
 248                         <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 249                                 <include name="${compbio-util}"/>
 250                                 <include name="${compbio-annotation}"/>
 251                         </zipgroupfileset>
 252                         <fileset refid="fullclient"/>
 253                         <manifest>
 254                                 <attribute name="Built-By" value="${author}" />
 255                                 <attribute name="Class-Path" value="." />
 256                                 <attribute name="Implementation-Title" value="JABAWS Core for ${product}" />
 257                                 <attribute name="Implementation-Vendor" value="${author}" />
 258                                 <attribute name="Implementation-URL" value="${project.url}" />
 259                         </manifest>
 260                 </jar>
 261         </target>
 262
 263         <target name="core-source-jar" depends="compile" description="Pack jabaws core java sources">
 264                 <delete file="${core-src}"></delete>
 265                 <jar jarfile="${core-src}">
 266                         <fileset dir="${basedir}/datamodel">
 267                                 <include name="**"/>
 268                         </fileset>
 269                         <fileset dir="${basedir}/engine">
 270                                 <include name="**"/>
 271                         </fileset>
 272                         <zipgroupfileset excludes="META-INF/*.MF" dir="${lib.path}/src">
 273                                 <include name="**"/>
 274                         </zipgroupfileset>
 275                         <manifest>
 276                                 <attribute name="Built-By" value="${author}" />
 277                                 <attribute name="Implementation-Title" value="${product} JABAWS Core Source Code Archive" />
 278                                 <attribute name="Implementation-Vendor" value="${author}" />
 279                                 <attribute name="Implementation-URL" value="${project.url}" />
 280                         </manifest>
 281                 </jar>
 282         </target>
 283
 284         <target name="jabaws-client-src-jar" depends="datamodel-source-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 285                 <echo>Jar file: JABAWS client source</echo>
 286                 <delete file="${jabaws-client-src}">
 287                 </delete>
 288                 <jar jarfile="${jabaws-client-src}">
 289                         <zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 290                         <fileset dir="${basedir}/webservices">
 291                                 <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
 292                                 <include name="compbio/data/msa/**"/>
 293                                 <exclude name="compbio/ws/client/ServicesUtil**"/>
 294                                 <exclude name="compbio/ws/client/AAConClient**"/>
 295                                 <include name="compbio/ws/client/**"/>
 296                         </fileset>
 297                         <manifest>
 298                                 <attribute name="Built-By" value="${author}" />
 299                                 <attribute name="Implementation-Title" value="${product} Client Source Code" />
 300                                 <attribute name="Implementation-Vendor" value="${author}" />
 301                                 <attribute name="Implementation-URL" value="${project.url}" />
 302                         </manifest>
 303                 </jar>
 304         </target>
 305
 306         <target name="minimal-jabaws-client-jar" depends="compile, datamodel-jar" description="Pack metadata, data model, WS interfaces, a simple ws client class">
 307                 <echo>Jar file: Minimal WS client jar</echo>
 308                 <delete file="${basedir}/${min-jabaws-client}"></delete>
 309                 <jar jarfile="${basedir}/${min-jabaws-client}">
 310                         <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
 311                         <fileset dir="${basedir}/WEB-INF/classes/">
 312                                 <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
 313                                 <include name="compbio/data/msa/**"/>
 314                                 <include name="compbio/ws/client/**"/>
 315                         </fileset>
 316                         <zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
 317                         <manifest>
 318                                 <attribute name="Built-By" value="${author}" />
 319                                 <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
 320                                 <attribute name="Class-Path" value="." />
 321                                 <attribute name="Implementation-Title" value="Minimal ${product} Client" />
 322                                 <attribute name="Implementation-Vendor" value="${author}" />
 323                                 <attribute name="Implementation-URL" value="${project.url}" />
 324                         </manifest>
 325                 </jar>
 326                 <delete file="${basedir}/${min-jabaws-client-nolog}"></delete>
 327                 <jar jarfile="${basedir}/${min-jabaws-client-nolog}">
 328                         <zipgroupfileset excludes="META-INF/*.SF" dir="" includes="${datamodel}" />
 329                         <fileset dir="${basedir}/WEB-INF/classes/">
 330                                 <!-- This will include JAXWS artifacts. Alternatively they can be generated on the fly. -->
 331                                 <include name="compbio/data/msa/**"/>
 332                                 <include name="compbio/ws/client/**"/>
 333                         </fileset>
 334                         <manifest>
 335                                 <attribute name="Built-By" value="${author}" />
 336                                 <attribute name="Main-Class" value="compbio.ws.client.Jws2Client" />
 337                                 <attribute name="Class-Path" value="." />
 338                                 <attribute name="Implementation-Title" value="Minimal ${product} Client" />
 339                                 <attribute name="Implementation-Vendor" value="${author}" />
 340                                 <attribute name="Implementation-URL" value="${project.url}" />
 341                         </manifest>
 342                 </jar>
 343         </target>
 344
 345
 346         <target name="stat-updater" depends="compile" description="Prepare executable jar for stat updater">
 347                 <echo>Jar file: StatUpdater jar</echo>
 348                 <delete file="${basedir}/${stat-updater}"></delete>
 349                 <copy file="${basedir}/log/log4j.properties.updater" tofile="${basedir}/log4j.properties"/>
 350                 <jar jarfile="${basedir}/${stat-updater}">
 351                         <fileset dir="${basedir}">
 352                                 <include name="log4j.properties"/>
 353                         </fileset>
 354                         <fileset refid="statupdater"/>
 355                         <zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/log4j-1.2.15.jar" />
 356                         <zipgroupfileset excludes="META-INF/*" dir="" includes="WEB-INF/lib/derby-10.8.2.2.jar" />
 357                         <zipgroupfileset excludes="META-INF/*" dir="" includes="lib/jcommander-1.30.jar" />
 358                         <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 359                                 <include name="${compbio-util}"/>
 360                         </zipgroupfileset>                      <manifest>
 361                                 <attribute name="Built-By" value="${author}" />
 362                                 <attribute name="Main-Class" value="compbio.stat.collector.ExecutionStatUpdater" />
 363                                 <attribute name="Class-Path" value="." />
 364                                 <attribute name="Implementation-Title" value="JABAWS Statistics Updating Program ${product}" />
 365                                 <attribute name="Implementation-Vendor" value="${author}" />
 366                                 <attribute name="Implementation-URL" value="${project.url}" />
 367                         </manifest>
 368                 </jar>
 369                 <delete file="${basedir}/log4j.properties"/>
 370         </target>
 371
 372         <target name="full-jabaws-client-jar" depends="compile" description="Pack datamodel, engine and runners">
 373                 <echo>Jar file: Full WS client jar</echo>
 374                 <delete file="${full-jabaws-client}">
 375                 </delete>
 376                 <jar jarfile="${full-jabaws-client}">
 377                         <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 378                                 <include name="${compbio-util}"/>
 379                                 <include name="${compbio-annotation}"/>
 380                                 <include name="drmaa.jar"/>
 381                         </zipgroupfileset>
 382                         <fileset refid="fullclient"/>
 383                         <manifest>
 384                                 <attribute name="Built-By" value="${author}" />
 385                                 <attribute name="Class-Path" value="." />
 386                                 <attribute name="Implementation-Title" value="Full ${product} Client" />
 387                                 <attribute name="Implementation-Vendor" value="${author}" />
 388                                 <attribute name="Implementation-URL" value="${project.url}" />
 389                         </manifest>
 390                 </jar>
 391         </target>
 392
 393         <target name="full-jabaws-client" depends="full-jabaws-client-jar, pack-binaries" description="Pack binaries with sources and configuration files">
 394                 <echo>Packing binaries, and configuration files</echo>
 395                 <zip destfile="${full-jabaws-client-pack}" >
 396                         <zipgroupfileset file="${binaries}" />
 397                         <zipfileset dir="conf" prefix="conf" >
 398                                 <exclude name="**/temp/**"/>
 399                         </zipfileset>
 400                         <fileset file="${full-jabaws-client}" />
 401                 </zip>
 402         </target>
 403
 404
 405         <target name="source-jar" depends="datamodel-source-jar" description="Pack java sources">
 406                 <delete file="${basedir}/${jabaws-source-jar}">
 407                 </delete>
 408                 <jar jarfile="${basedir}/${jabaws-source-jar}">
 409                         <zipgroupfileset  excludes="META-INF/*.MF" file="${datamodel-src}"/>
 410                         <fileset dir="${basedir}/runner">
 411                                 <include name="**"/>
 412                         </fileset>
 413                         <fileset dir="${basedir}/engine">
 414                                 <include name="**"/>
 415                         </fileset>
 416                         <fileset dir="${basedir}/webservices/">
 417                                 <include name="**"/>
 418                         </fileset>
 419                         <manifest>
 420                                 <attribute name="Built-By" value="${author}" />
 421                                 <attribute name="Class-Path" value="." />
 422                                 <attribute name="Implementation-Title" value="${product} Source Code Archive" />
 423                                 <attribute name="Implementation-Vendor" value="${author}" />
 424                                 <attribute name="Implementation-URL" value="${project.url}" />
 425                         </manifest>
 426                 </jar>
 427         </target>
 428
 429         <target name="full-jabaws-jar" depends="compile" description="Pack datamodel, engine, runners, configuration, binaries and webservices">
 430                 <echo>Jar file: Full WS client jar</echo>
 431                 <delete file="${full-jabaws-client}">
 432                 </delete>
 433                 <jar jarfile="${full-jabaws-client}">
 434                         <zipgroupfileset excludes="META-INF/*.SF" dir="${web.lib.path}" >
 435                                 <include name="log4j-1.2.15.jar"/>
 436                                 <include name="${compbio-util}"/>
 437                                 <include name="${compbio-annotation}"/>
 438                                 <include name="drmaa.jar"/>
 439                         </zipgroupfileset>
 440                         <fileset refid="fullclient">
 441                         </fileset>
 442                         <fileset dir="${basedir}/WEB-INF/classes/">
 443                                 <!-- Statistics web application -->
 444                                 <include name="compbio/stat/**"/>
 445                                 <!-- Web services-->
 446                                 <include name="compbio/ws/**"/>
 447                         </fileset>
 448                         <!-- Set WSTester as main to help user to test their deployments -->
 449                         <manifest>
 450                                 <attribute name="Built-By" value="${author}" />
 451                                 <attribute name="Class-Path" value="." />
 452                                 <attribute name="Main-Class" value="compbio.ws.client.WSTester" />
 453                                 <attribute name="Implementation-Title" value="${product}" />
 454                                 <attribute name="Implementation-Vendor" value="${author}" />
 455                                 <attribute name="Implementation-URL" value="${project.url}" />
 456                         </manifest>
 457                 </jar>
 458         </target>
 459
 460         <target name="pack-binaries" description="Zip all binary files">
 461                 <delete file="${binaries}" failonerror="false"/>
 462                 <zip destfile="${binaries}" >
 463                         <zipfileset dir="${basedir}/binaries" prefix="binaries" excludes="**/linux*/**"/>
 464                 </zip>
 465         </target>
 466
 467         <target name="jabaws-no-binaries" depends="full-jabaws-jar, clearStatDB" description="Prepare JABAWS war file without native binaries">
 468                 <echo>Preparing a war file without binaries</echo>
 469                 <delete file="${jabaws-no-binaries}">
 470                 </delete>
 471                 <zip destfile="${jabaws-no-binaries}" whenempty="create">
 472                         <zipfileset dir="${basedir}/WEB-INF" prefix="WEB-INF">
 473                                 <exclude name="classes"/>
 474                                 <!-- These are included into JABA client so exclude the jars -->
 475                                 <exclude name="lib/drmaa.jar"/>
 476                                 <exclude name="lib/log4j-1.2.15.jar"/>
 477                                 <exclude name="lib/${compbio-annotation}"/>
 478                                 <exclude name="lib/${compbio-util}"/>
 479
 480                                 <include name="web.xml"/>
 481                                 <include name="sun-jaxws.xml"/>
 482                                 <include name="lib/*"/>
 483                         </zipfileset>
 484                         <zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
 485                         <zipfileset dir="${basedir}/statpages" prefix="statpages" />
 486                         <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
 487                         <zipfileset dir="conf" prefix="conf" >
 488                                 <exclude name="**/temp/**"/>
 489                         </zipfileset>
 490                         <!-- Add JABAWS web site apart from the binary archive -->
 491                         <zipfileset dir="${basedir}/website" excludes="archive/**, devel*.html, tests/**, template.html"/>
 492                         <zipfileset dir="." includes="${full-jabaws-client}" fullpath="WEB-INF/lib/jabaws-client.jar"/>
 493                         <!-- Put a copy of log4j configuration file where it can be used  -->
 494                         <zipfileset dir="log" includes="log4j.properties" prefix="WEB-INF/classes"/>
 495                 </zip>
 496         </target>
 497
 498         <target name="build-devel-website" description="Pack developement related pages, tests, javadoc" >
 499                 <echo>Packing data for internal web site</echo>
 500                 <delete file="${jabaws-devel-web}">
 501                 </delete>
 502                 <zip destfile="${jabaws-devel-web}" whenempty="create">
 503                         <!-- Add JABAWS web site apart from the binary archive -->
 504                         <zipfileset dir="${basedir}/website" excludes="template.html, download.html, index.html, manual.html, howto.html, archive/**, prog_docs/**"/>
 505                 </zip>
 506         </target>
 507
 508         <target name="jabaws-complete" depends="jabaws-no-binaries, pack-binaries" description="Prepare JABAWS war file without runtime dependency - JAXWS jars">
 509                 <echo>Preparing a complete war file</echo>
 510                 <delete file="${jabaws}">
 511                 </delete>
 512                 <copy tofile="${jabaws}" file="${jabaws-no-binaries}"/>
 513                 <zip destfile="${jabaws}" update="true" >
 514                         <zipgroupfileset file="${binaries}" />
 515                 </zip>
 516         </target>
 517
 518         <target name="build-all" depends="full-jabaws-client, minimal-jabaws-client-jar, jabaws-no-binaries, jabaws-complete, datamodel-jar, datamodel-source-jar, core-jar, core-source-jar, source-jar, jabaws-client-src-jar" description="Build-all the distributives"/>
 519
 520         <!-- This task does not really depends on compile, but it is better to make sure that the code is sound -->
 521         <target name="archive-project" description="Pack everything in the project for those who do not have access to SVN" depends="compile">
 522                 <delete file="${jabaws-project}">
 523                 </delete>
 524                 <zip destfile="${jabaws-project}" whenempty="create" >
 525                         <fileset dir="." excludes="${distdir}/**, jobsout/**, test-output/**, **.svn, dundee-conf/**, TODO.txt, IDEAS.txt, ${activity.log}, **/*.zip, **/*.war"/>
 526                         <!-- Add jobsout directory but no content -->
 527                         <zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="*/**"/>
 528                 </zip>
 529         </target>
 530
 531 <!-- ####################################################################################################################################### -->
 532 <!-- Test targets -->
 533         <taskdef name="testNG" classname="org.testng.TestNGAntTask">
 534                 <classpath refid="test.classpath">
 535                 </classpath>
 536         </taskdef>
 537
 538         <target name="CustomTest" depends="compile_with_debug">
 539                 <delete file="${activity.log}"/>
 540                 <testNG haltonfailure="true" enableassert="true" >
 541                         <jvmarg value="-server" />
 542                         <jvmarg value="-enableassertions" />
 543                         <jvmarg value="-Xms1024m" />
 544                         <jvmarg value="-Xmx1024m" />
 545                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 546                         <classpath refid="test.classpath" />
 547                         <classpath refid="project.classpath" />
 548                         <xmlfileset dir="." includes="temp-testng-customsuite.xml"/>
 549                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 550                 </testNG>
 551         </target>
 552
 553         <target name="Run_cluster_dependent_test" depends="compile_with_debug">
 554                 <delete file="${activity.log}"/>
 555                 <testNG groups="cluster" haltonfailure="true" enableassert="true" parallel="false" verbose="3">
 556                         <jvmarg value="-server" />
 557                         <jvmarg value="-enableassertions" />
 558                         <jvmarg value="-Xms1024m" />
 559                         <jvmarg value="-Xmx1024m" />
 560                         <classfileset dir="${classes}" includes="**/*.class" />
 561                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 562                         <classpath refid="test.classpath" />
 563                         <classpath refid="project.classpath" />
 564                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 565                 </testNG>
 566         </target>
 567
 568         <target name="Test" depends="compile_with_debug">
 569                 <delete file="${activity.log}"/>
 570                 <testNG haltonfailure="true" enableassert="true" verbose="3" excludedgroups="performance, webservices" >
 571                         <jvmarg value="-server" />
 572                         <jvmarg value="-enableassertions" />
 573                         <jvmarg value="-Xms1024m" />
 574                         <jvmarg value="-Xmx1024m" />
 575                         <classfileset dir="${classes}" includes="**/*.class" />
 576                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 577                         <classpath refid="test.classpath" />
 578                         <classpath refid="project.classpath" />
 579                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 580                 </testNG>
 581         </target>
 582
 583         <target name="Performance_tests" depends="compile_with_debug">
 584                 <delete file="${activity.log}"/>
 585                 <testNG haltonfailure="true" enableassert="true" verbose="3" groups="performance" >
 586                         <jvmarg value="-server" />
 587                         <jvmarg value="-enableassertions" />
 588                         <jvmarg value="-Xms1024m" />
 589                         <jvmarg value="-Xmx1024m" />
 590                         <classfileset dir="${classes}" includes="**/*.class" />
 591                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 592                         <classpath refid="test.classpath" />
 593                         <classpath refid="project.classpath" />
 594                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 595                 </testNG>
 596         </target>
 597
 598         <target name="Test_runners" depends="compile_with_debug">
 599                 <delete file="${activity.log}"/>
 600                 <testNG groups="runner" haltonfailure="true" verbose="3" enableassert="true" >
 601                         <jvmarg value="-server" />
 602                         <jvmarg value="-enableassertions" />
 603                         <jvmarg value="-Xms1024m" />
 604                         <jvmarg value="-Xmx1024m" />
 605                         <classfileset dir="${classes}" includes="**/*.class" />
 606                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 607                         <classpath refid="test.classpath" />
 608                         <classpath refid="project.classpath" />
 609                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 610                 </testNG>
 611         </target>
 612
 613         <target name="Test_engines" depends="compile_with_debug">
 614                 <delete file="${activity.log}"/>
 615                 <testNG groups="engine" haltonfailure="true" verbose="3" enableassert="true" >
 616                         <jvmarg value="-server" />
 617                         <jvmarg value="-enableassertions" />
 618                         <jvmarg value="-Xms1024m" />
 619                         <jvmarg value="-Xmx1024m" />
 620                         <classfileset dir="${classes}" includes="**/*.class" />
 621                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 622                         <classpath refid="test.classpath" />
 623                         <classpath refid="project.classpath" />
 624                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 625                 </testNG>
 626         </target>
 627
 628         <target name="All_cluster_independent_windows_only_tests" depends="compile_with_debug">
 629                 <delete file="${activity.log}" failonerror="false"/>
 630                 <testNG excludedgroups="cluster, non_windows" haltonfailure="true" verbose="3" enableassert="true"  >
 631                         <jvmarg value="-server" />
 632                         <jvmarg value="-enableassertions" />
 633                         <jvmarg value="-Xms1024m" />
 634                         <jvmarg value="-Xmx1024m" />
 635                         <classfileset dir="${classes}" includes="**/*.class" />
 636                         <classpath refid="test.classpath" />
 637                         <classpath refid="project.classpath" />
 638                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 639                 </testNG>
 640         </target>
 641
 642         <target name="All_cluster_independent_tests" depends="compile_with_debug">
 643                 <delete file="${activity.log}" failonerror="false"/>
 644                 <testNG excludedgroups="cluster, performance" haltonfailure="true" verbose="3" enableassert="true"  >
 645                         <jvmarg value="-server" />
 646                         <jvmarg value="-enableassertions" />
 647                         <jvmarg value="-Xms1024m" />
 648                         <jvmarg value="-Xmx1024m" />
 649                         <classfileset dir="${classes}" includes="**/*.class" />
 650                         <classpath refid="test.classpath" />
 651                         <classpath refid="project.classpath" />
 652                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 653                 </testNG>
 654         </target>
 655
 656         <target name="Rerun_failed_tests" depends="compile_with_debug">
 657                 <delete file="${activity.log}" failonerror="false"/>
 658                 <testNG haltonfailure="true" enableassert="true" verbose="9" >
 659                         <jvmarg value="-server" />
 660                         <jvmarg value="-enableassertions" />
 661                         <jvmarg value="-Xms1024m" />
 662                         <jvmarg value="-Xmx1024m" />
 663                         <env key="LD_LIBRARY_PATH" value="${LD_LIBRARY_PATH}"/>
 664                         <classpath refid="test.classpath" />
 665                         <classpath refid="project.classpath" />
 666                         <xmlfileset dir="." includes="test-output/testng-failed.xml"/>
 667                         <sysproperty key="TestingDataPath" value="${data.src}"/>
 668                 </testNG>
 669         </target>
 670 </project>