Changeset 1383


Ignore:
Timestamp:
Aug 22, 2011, 3:38:32 PM (10 years ago)
Author:
Martin Svensson
Message:

Fixes #312 Updates required for BASE 3 support. Downloading the necessary base3-jar files with Ant has not been cause the base3 has not been released yet.

Location:
extensions/net.sf.basedb.mev/trunk
Files:
11 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.mev/trunk

    • Property svn:ignore
      •  

        old new  
        44build.properties
        55.project
         6mev-launcher.jar
  • extensions/net.sf.basedb.mev/trunk/.classpath

    r1163 r1383  
    55  <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
    66  <classpathentry kind="lib" path="lib/compile/servlet-api.jar"/>
    7   <classpathentry kind="lib" path="lib/compile/BASE2CorePlugins.jar"/>
    8   <classpathentry kind="lib" path="lib/compile/BASE2Webclient.jar"/>
    9   <classpathentry kind="lib" path="lib/compile/BASE2WSClient.jar"/>
    10   <classpathentry kind="lib" path="lib/compile/BASE2Core.jar" sourcepath="/trunk/src/core"/>
    117  <classpathentry kind="lib" path="resources/jar/mev-base.jar" sourcepath="/mev-4.4.1/source"/>
    128  <classpathentry kind="lib" path="resources/jar/mev-gui-impl.jar" sourcepath="/mev-4.4.1/source"/>
    139  <classpathentry kind="lib" path="resources/jar/HTTPClient.jar"/>
     10  <classpathentry kind="lib" path="lib/compile/base-core-3.0.0.jar"/>
     11  <classpathentry kind="lib" path="lib/compile/base-coreplugins-3.0.0.jar"/>
     12  <classpathentry kind="lib" path="lib/compile/base-webclient-3.0.0.jar"/>
     13  <classpathentry kind="lib" path="lib/compile/base-webservices-client-3.0.0.jar"/>
    1414  <classpathentry kind="output" path="bin"/>
    1515</classpath>
  • extensions/net.sf.basedb.mev/trunk/META-INF/extensions.xml

    r1264 r1383  
    99    </description>
    1010    <version>1.8pre</version>
    11     <copyright>BASE 2 development team</copyright>
     11    <copyright>BASE development team</copyright>
    1212    <email>basedb-users@lists.sourceforge.net</email>
    1313    <url>http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev</url>
     14    <min-base-version>3.0.0</min-base-version>   
    1415  </about>
     16  <plugin-definition id="PackageInstaller">
     17    <about>
     18      <name>MeV package installer</name>
     19      <description>
     20        This plug-in will install required data files types, etc. that
     21        are required to use the MeV launcher and plug-ins. Start the installation by
     22        selecting this plug-in from the list at Administrate -> Plugins -> Definitions.
     23        Then click on the 'Run plugin' button.
     24      </description>
     25    </about>
     26    <plugin-class>net.sf.basedb.mev.install.Install</plugin-class>
     27  </plugin-definition>
     28  <plugin-definition id="CghExporterPlugin">
     29    <about>
     30      <name>MeV CGH exporter</name>     
     31      <description>
     32        MeV CGH exporter Comparative Genomic Hybridization exporter for bioassay set data.
     33        The resulting file can be opened in MeV for further analysis.
     34      </description>
     35    </about>   
     36    <plugin-class>net.sf.basedb.mev.plugin.CghExporterPlugin</plugin-class>
     37  </plugin-definition>
     38  <plugin-definition id="TdmsExporterPlugin">
     39    <about>
     40      <name>MeV TDMS exporter</name>
     41      <description>
     42        Tab-delimited Multiple Sample exporter for bioassay set data.
     43        The resulting file can be opened in MeV for further analysis.
     44      </description>     
     45    </about>   
     46    <plugin-class>net.sf.basedb.mev.plugin.TdmsExporterPlugin</plugin-class>
     47  </plugin-definition>
    1548  <extension
    1649    id="net.sf.basedb.mev.launchmev"
     
    6598      </parameters>
    6699    </action-factory>
    67   </extension>
     100  </extension> 
    68101</extensions>
  • extensions/net.sf.basedb.mev/trunk/README

    r1294 r1383  
    11== Requirements ==
    22
    3  1. BASE 2.17.0 or later.
     3 1. BASE 3.0 or later.
    44 
    55== Introduction ==
     
    1919 1. Download the mev-launcher-*.tar.gz file.
    2020 2. Unpack the downloaded file to a directory of your choice.
    21  3. Copy the mev-launcher.jar file to your BASE extensions directory:
    22     WEB-INF/extensions.
    23  4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
    24     installation. Otherwise, just wait a bit and the automatic installation will
    25     find and install the new extension.
    26  5. Run the plug-in installation wizard by clicking the 'New' button on the
    27     'Administrate -> Plugins -> Definitions' page. Make sure the option for
    28     the 'Extensions directory' is selected. Install all plug-ins found in
    29     the mev-launcher.jar file.
     21 3. Copy the mev-launcher.jar file to your BASE plug-ins directory. Look in
     22  your 'base.config' file if you don't know where this is.
     23 4. Go to 'Administrate->Plug-ins & Extensions->Overview' page.
     24 5. Run the installation wizard and select to install 'mev-launcher.jar'.
    3025 6. Run the 'MeV package installer' plug-in. Find this plug-in on the
    3126    'Administrate -> Plugins -> Definitions' page, click on it, and then
     
    7267 2. Type `ant download-lib` to automatically download the BASE core JAR files that
    7368    are neeed for compilation. You can also do this manually by copying the
    74     BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar
     69    base-core-3.0.0.jar, base-webclient-3.0.0.jar, base-coreplugins-3.0.0.jar and base-webservices-client-3.0.0.jar
    7570    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the
    7671    ./lib/compile directory.
  • extensions/net.sf.basedb.mev/trunk/build.xml

    r1294 r1383  
    2525  <property name="javac.target" value="1.6" />
    2626  <property name="javac.encoding" value="UTF-8" />
    27   <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.17.0" />
     27  <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/" />
    2828
    2929  <!-- set up classpath for compiling -->
     
    193193  <target
    194194    name="checkjar"
    195     description="Checks that the BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar exists."
     195    description="Checks that the base-core-3.0.0.jar, base-webclient-3.0.0.jar, base-coreplugins-3.0.0.jar and base-webservices-client-3.0.0.jar exists."
    196196    >
    197197    <available classname="net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter"
    198       classpathref="classpath" property="base2core" />
     198      classpathref="classpath" property="basecore" />
    199199    <available classname="net.sf.basedb.plugins.util.Parameters"
    200       classpathref="classpath" property="base2plugins" />
     200      classpathref="classpath" property="baseplugins" />
    201201    <available classname="net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory"
    202       classpathref="classpath" property="base2web" />
     202      classpathref="classpath" property="baseweb" />
    203203    <available classname="net.sf.basedb.info.BioAssaySetInfo"
    204       classpathref="classpath" property="base2webservice" />
    205     <fail unless="base2core" message="Can't find BASE2Core.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
    206     <fail unless="base2plugins" message="Can't find BASE2CorePlugins.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
    207     <fail unless="base2web" message="Can't find BASE2Webclient.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
    208     <fail unless="base2webservice" message="Can't find BASE2WSClient.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
    209     <echo>Found BASE2Core.jar, BASE2CorePlugins.jar, BASE2Webclient.jar and BASE2WSClient.jar.</echo>
     204      classpathref="classpath" property="basewebservice" />
     205    <fail unless="basecore" message="Can't find base-core-3.0.0.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     206    <fail unless="baseplugins" message="Can't find base-coreplugins-3.0.0.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     207    <fail unless="baseweb" message="Can't find base-webclient-3.0.0.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     208    <fail unless="basewebservice" message="Can't find base-webservices-client-3.0.0.jar in ./lib/compile. Try 'ant download-lib' to download the missing file." />
     209    <echo>Found base-core-3.0.0.jar, base-coreplugins-3.0.0.jar, base-webclient-3.0.0.jar and base-webservices-client-3.0.0.jar.</echo>
    210210  </target>
    211211 
     
    251251  <target
    252252    name="download-lib"
    253     description="Download BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar"
     253    description="Download base-core-3.0.0.jar, base-webclient-3.0.0.jar, base-coreplugins-3.0.0.jar and base-webservices-client-3.0.0.jar"
    254254    >
    255255    <echo>
     
    260260-------------------------------------------------------
    261261    </echo>
    262     <download-lib file="BASE2Core.jar" />
    263     <download-lib file="BASE2CorePlugins.jar" />
    264     <download-lib file="BASE2Webclient.jar" />
    265     <download-lib file="BASE2WSClient.jar" />
     262    <download-lib file="base-core-3.0.0.jar" />
     263    <download-lib file="base-webclient-3.0.0.jar" />
     264    <download-lib file="base-coreplugins-3.0.0.jar" />
     265    <download-lib file="base-webservices-client-3.0.0.jar" />
    266266  </target>
    267267 
  • extensions/net.sf.basedb.mev/trunk/lib/compile

    • Property svn:ignore
      •  

        old new  
        11BASE2*.jar
         2base-core-3.0.0.jar
         3base-coreplugins-3.0.0.jar
         4base-webclient-3.0.0.jar
         5base-webservices-client-3.0.0.jar
  • extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/Mev.java

    r1264 r1383  
    88*/
    99public class Mev
    10 {
    11   /**
    12     The current version of this plug-in package.
    13   */
    14   public static final String VERSION = "1.8pre";
    15  
    16   /**
    17     The URL where more information about this plug-in package can
    18     be found.
    19   */
    20   public static final String URL = "http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev";
    21  
    22   /**
    23     The copyright holders of the plug-ins.
    24   */
    25   public static final String COPYRIGHT = "BASE 2 development team";
    26  
    27   /**
    28     The email address to use for support and more information.
    29   */
    30   public static final String EMAIL = "basedb-users@lists.sourceforge.net";
    31 
     10{
    3211  /**
    3312    The external ID for the file type representing
  • extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/factory/MevButtonFactory.java

    r1227 r1383  
    8888      boolean hasWritePermission = bas.hasPermission(Permission.WRITE);
    8989      boolean createAction = true;
    90       if (getRequireMevFile() != null) createAction &= hasAccessibleMevFile(dc, bas, getRequireMevFile());
     90      if (getRequireMevFile() != null) createAction &= hasAccessibleMevFile(dc, bas, getRequireMevFile(), true);
    9191      if (getRequireSpotData() != null) createAction &= getRequireSpotData() == hasSpotData;
    9292      if (getRequireWritePermission() != null) createAction &= getRequireWritePermission() == hasWritePermission;
     
    159159  }
    160160 
    161   private boolean hasAccessibleMevFile(DbControl dc, BioAssaySet bas, String fileType)
     161  private boolean hasAccessibleMevFile(DbControl dc, BioAssaySet bas, String fileType, boolean requireValid)
    162162  {
    163163    File mevFile = null;
    164164    try
    165165    {
    166       mevFile = FileStoreUtil.getDataFile(dc, bas, fileType);
     166      mevFile = FileStoreUtil.getDataFile(dc, bas, fileType, requireValid);
    167167      if (mevFile != null)
    168168      {
  • extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/install/Install.java

    r1180 r1383  
    2626import net.sf.basedb.core.DataFileType;
    2727import net.sf.basedb.core.DbControl;
    28 import net.sf.basedb.core.FileType;
     28import net.sf.basedb.core.File;
     29import net.sf.basedb.core.ItemSubtype;
    2930import net.sf.basedb.core.Group;
    3031import net.sf.basedb.core.GroupPermissions;
     
    9091  extends AbstractPlugin
    9192  implements InteractivePlugin
    92 {
    93   private static final About about = new AboutImpl(
    94     "MeV package installer",
    95     "This plug-in will install required data files types, etc. that " +
    96     "are required to use the MeV launcher and plug-ins. Start the installation by " +
    97     "selecting this plug-in from the list at Administrate -> Plugins -> Definitions. " +
    98     "Then click on the 'Run plugin' button.",
    99     Mev.VERSION,
    100     Mev.COPYRIGHT,
    101     null,
    102     Mev.EMAIL,
    103     Mev.URL
    104   );
    105  
     93{
    10694  private static final Set<GuiContext> guiContexts =
    10795    Collections.singleton(new GuiContext(Item.PLUGINDEFINITION, GuiContext.Type.ITEM));
     
    115103    From the Plugin interface
    116104    -------------------------------------------
    117   */
    118   public About getAbout()
    119   {
    120     return about;
    121   }
     105  */ 
    122106  @Override
    123107  public boolean supportsConfigurations()
     
    232216    try
    233217    {
    234       FileType spotDataType = FileType.getById(dc, SystemItems.getId(net.sf.basedb.core.FileType.SPOT_DATA));
     218      ItemSubtype spotDataType = ItemSubtype.getById(dc, SystemItems.getId(File.SPOT_DATA));
    235219
    236220      // MIME type
     
    246230      DataFileType mevAnalysisFile = createDataFileType(dc, Mev.ANALYSIS_FILE, "MeV analysis file",
    247231        "A MeV analysis file",
    248         Item.BIOASSAYSET, "anl", spotDataType, null, null, null);
     232        Item.BIOASSAYSET, "anl", spotDataType);
    249233      createDataFileType(dc, Mev.CGH_FILE, "MeV CGH",
    250234        "A MeV Comparative Genomic Hybridization file",
    251         Item.BIOASSAYSET, null, spotDataType, null, null, null);
     235        Item.BIOASSAYSET, null, spotDataType);
    252236      createDataFileType(dc, Mev.TDMS_FILE, "MeV TDMS",
    253237        "A MeV Tab-Delimited Multiple Sample file",
    254         Item.BIOASSAYSET, null, spotDataType, null, null, null);
     238        Item.BIOASSAYSET, null, spotDataType);
    255239      dc.commit();
    256240
     
    354338  */
    355339  private DataFileType createDataFileType(DbControl dc, String externalId, String name,
    356       String description, Item itemType, String extension, FileType genericType,
    357       String validatorClass, String metadataReaderClass, String jarPath)
     340      String description, Item itemType, String extension, ItemSubtype genericType)
    358341    throws ItemAlreadyExistsException
    359342  {   
     
    361344    try
    362345    {
    363       dft = DataFileType.getByExternalId(dc, externalId);
    364      
    365       // Update the jar path of the data file type's meta-data reader and validator
    366       if (jarPath != null)
    367       {
    368         dft.setMetadataReaderJarPath(jarPath);
    369         dft.setValidatorJarPath(jarPath);
    370       }
     346      dft = DataFileType.getByExternalId(dc, externalId);     
    371347    }
    372348    catch (ItemNotFoundException infe)
     
    377353      dft.setExtension(extension);
    378354      dft.setDescription(description);
    379       dft.setGenericType(genericType);
    380       dft.setValidatorClass(validatorClass);
    381       dft.setValidatorJarPath(jarPath);
    382       dft.setMetadataReaderClass(metadataReaderClass);
    383       dft.setMetadataReaderJarPath(jarPath);
     355      dft.setGenericType(genericType);     
    384356    }
    385357    return dft;
  • extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/plugin/CghExporterPlugin.java

    r1294 r1383  
    6969    From the Plugin interface
    7070    -------------------------------------------
    71   */
    72   @Override
    73   public About getAbout()
    74   {
    75     return new AboutImpl(
    76         "MeV CGH exporter",
    77         "Comparative Genomic Hybridization exporter for bioassay set data. The " +
    78         "resulting file can be opened in MeV for further analysis.",
    79         Mev.VERSION,
    80         Mev.COPYRIGHT,
    81         null,
    82         Mev.EMAIL,
    83         Mev.URL
    84       );
    85   }
     71  */ 
    8672  @Override
    8773  public boolean supportsConfigurations()
  • extensions/net.sf.basedb.mev/trunk/src/server/net/sf/basedb/mev/plugin/TdmsExporterPlugin.java

    r1294 r1383  
    6565  */
    6666  @Override
    67   public About getAbout()
    68   {
    69     return new AboutImpl(
    70         "MeV TDMS exporter",
    71         "Tab-delimited Multiple Sample exporter for bioassay set data. The " +
    72         "resulting file can be opened in MeV for further analysis.",
    73         Mev.VERSION,
    74         Mev.COPYRIGHT,
    75         null,
    76         Mev.EMAIL,
    77         Mev.URL
    78       );
    79   }
    80   @Override
    8167  public boolean supportsConfigurations()
    8268  {
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