Changeset 391


Ignore:
Timestamp:
Aug 14, 2007, 4:48:31 PM (14 years ago)
Author:
dominic
Message:

added ebi-utils jar and new build filefor affy plugin

Location:
trunk/uk/ac/ebi/AffyArrayDesignBatchImporter
Files:
6 added
1 deleted
3 edited

Legend:

Unmodified
Added
Removed
  • trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/build.xml

    r382 r391  
    66  <property name="bin.plugins" location="bin" />
    77  <property name="lib.plugins" location="lib" />
     8  <property name="util.src.plugins" location="${src.plugins}/uk/ac/ebi/nugo/common" />
     9  <property name="core.src.plugins" location="${src.plugins}/uk/ac/ebi/nugo/plugins" />
    810 
    911  <property name="javac.arg" value="-Xlint:unchecked"
    1012      description="Extra arguments sent to Java compiler" />
    1113  <property name="plugin.name" value="AffyArrayDesignBatchImporter" />
     14  <property name="utils.name" value="ebi-plugins-utils" />
    1215 
    1316  <!-- set up classpath for compiling -->
     
    2023    <target
    2124      name="build.plugin"
    22       depends="nutriplugin.compile"
     25      depends="utils,nutriplugin.compile"
    2326      description="Compile the plugin"
    24     />
     27  />
     28 
     29  <target name="utils"
     30      depends=""
     31      description="compile the common ebi -plugin util classes"
     32      >
     33      <javac
     34        encoding="ISO-8859-1"
     35        srcdir="${util.src.plugins}"
     36        destdir="${bin.plugins}"
     37        classpathref="nugo.plugin.compile.classpath"
     38        debug="true"
     39        deprecation="true"
     40        >
     41        <compilerarg value="${javac.arg}" />
     42      </javac>
     43      <jar
     44        basedir="${bin.plugins}"
     45        jarfile="${lib.plugins}\ebi-plugins-utils.jar"
     46      />
     47      <jar
     48        basedir="${bin.plugins}"
     49        jarfile="${utils.name}.jar"
     50      />
     51      <delete includeemptydirs="true">
     52        <fileset dir="${bin.plugins}" includes="**/*"/>
     53      </delete>
     54    </target>
    2555   
    2656  <target
     
    3161      <javac
    3262        encoding="ISO-8859-1"
    33         srcdir="${src.plugins}"
     63        srcdir="${core.src.plugins}"
    3464        destdir="${bin.plugins}"
    3565        classpathref="nugo.plugin.compile.classpath"
  • trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/src/uk/ac/ebi/nugo/plugins/AffyArrayDesignBatchImporter.java

    r382 r391  
    4040import net.sf.basedb.core.plugin.Request;
    4141import net.sf.basedb.core.plugin.Response;
     42import uk.ac.ebi.nugo.common.*;
    4243import uk.ac.ebi.nugo.plugins.lims.AffymetrixFileFormatTypes;
    43 import uk.ac.ebi.nugo.plugins.util.AffyHelper;
    44 import uk.ac.ebi.nugo.plugins.util.AffyZipUnpacker;
     44
    4545
    4646/**
     
    216216        Unpack Zip files
    217217       */
    218       AffyZipUnpacker affyArrayDesignUnpacker = new AffyZipUnpacker(file, user, sc);
     218      ZipUnpacker affyArrayDesignUnpacker = new ZipUnpacker(file, user, sc);
    219219      affyArrayDesignUnpacker.unpack();
    220220      /*
     
    231231      {
    232232        // get the file extension and filename
    233         String ext= AffyHelper.getFileExtension(affyFile);
     233        String ext= Helper.getFileExtension(affyFile);
    234234       
    235235        //  check for validity against an enum file
     
    253253        String fileName = affyFile.getName();
    254254        String fileNameWithoutExtension = fileName.substring(0, fileName.indexOf("."));
    255               ArrayDesign ad= AffyHelper.getArrayDesign(fileNameWithoutExtension, dc);
     255              ArrayDesign ad= Helper.getArrayDesign(fileNameWithoutExtension, dc);
    256256              //if no array design was found create a new one otherwise
    257257              //skip array design creation
     
    278278      {
    279279        response.setError(ex.getMessage(), Arrays.asList(ex));
    280        
    281280      }
    282281      finally
     
    302301      catch (Exception e)
    303302      {
    304          return false;
    305       }
     303        Helper.write("File is not a zip file and cannot be imported by this plugin.");
     304        return false;
     305      }
    306306      finally
    307307      {
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