Changeset 6758


Ignore:
Timestamp:
Feb 23, 2015, 9:43:11 AM (7 years ago)
Author:
Nicklas Nordborg
Message:

References #1325: Lists of items (similar funcion as biomaterial lists)

Removing BioMaterialList class. Deprecating classes in package 'net.sf.basedb.util.biomaterial' since I think they need to be replaced with a better solution for walking up/down parent/child relationships.

Location:
trunk/src
Files:
2 deleted
10 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/core/net/sf/basedb/core/Item.java

    r6756 r6758  
    357357      470),
    358358     
    359   /**
    360     The item is a {@link BioMaterialList}
    361   */
    362   @Deprecated
    363   BIOMATERIALLIST(2090, "Biomaterial list", "bml", BioMaterialList.class, BioMaterialListData.class, DefinedPermissions.shareable,
    364       480),
    365 
    366359  /**
    367360    The item is a {@link BioPlateType}.
  • trunk/src/core/net/sf/basedb/core/data/BioMaterialData.java

    r6281 r6758  
    123123  }
    124124
    125   private Set<BioMaterialListData> lists;
    126   /**
    127     This is the inverse end.
    128     NOTE! We do not map with inverse="true" since we want automatic
    129     deletion from the join table when a biomaterial is deleted.
    130     @see BioMaterialListData#getBioMaterials()
    131     @since 2.10
    132     @hibernate.set lazy="true" table="`BioMaterialListMembers`"
    133     @hibernate.collection-key column="`biomaterial_id`"
    134     @hibernate.collection-many-to-many column="`list_id`" class="net.sf.basedb.core.data.BioMaterialListData"
    135   */
    136   Set<BioMaterialListData> getBioMaterialLists()
    137   {
    138     return lists;
    139   }
    140   void setBioMaterialLists(Set<BioMaterialListData> lists)
    141   {
    142     this.lists = lists;
    143   }
    144  
    145125  private Set<BioMaterialEventSourceData> childCreationEvents;
    146126  /**
  • trunk/src/core/net/sf/basedb/util/biomaterial/BioSourceToSampleTransformer.java

    r4723 r6758  
    4646  @base.modified $Date$
    4747*/
     48@Deprecated
    4849public class BioSourceToSampleTransformer
    4950  implements CollectionTransformer<BioSource, Sample>
  • trunk/src/core/net/sf/basedb/util/biomaterial/ChildrenTransformer.java

    r5689 r6758  
    4646  @base.modified $Date$
    4747*/
     48@Deprecated
    4849public class ChildrenTransformer<I extends MeasuredBioMaterial>
    4950  implements CollectionTransformer<I, I>
  • trunk/src/core/net/sf/basedb/util/biomaterial/ExtractToSampleTransformer.java

    r5663 r6758  
    5353  @base.modified $Date$
    5454*/
     55@Deprecated
    5556public class ExtractToSampleTransformer
    5657  implements CollectionTransformer<Extract, Sample>
  • trunk/src/core/net/sf/basedb/util/biomaterial/ListUtil.java

    r5663 r6758  
    3131import net.sf.basedb.core.BaseException;
    3232import net.sf.basedb.core.BioMaterial;
    33 import net.sf.basedb.core.BioMaterialList;
    3433import net.sf.basedb.core.BioSource;
    3534import net.sf.basedb.core.DbControl;
     
    3736import net.sf.basedb.core.InvalidDataException;
    3837import net.sf.basedb.core.Item;
     38import net.sf.basedb.core.ItemList;
    3939import net.sf.basedb.core.ItemQuery;
    4040import net.sf.basedb.core.PermissionDeniedException;
     
    5151  @base.modified $Date$
    5252*/
     53@Deprecated
    5354public class ListUtil
    5455{
     
    102103      write permission for the list
    103104  */
    104   public static <S extends BioMaterial> int addToList(BioMaterialList list,
     105  public static <S extends BioMaterial> int addToList(ItemList list,
    105106    Collection<? extends S> sources,
    106107    CollectionTransformer<S, ? extends BioMaterial> transformer)
  • trunk/src/core/net/sf/basedb/util/biomaterial/ParentsTransformer.java

    r5689 r6758  
    4646  @base.modified $Date$
    4747*/
     48@Deprecated
    4849public class ParentsTransformer<I extends MeasuredBioMaterial>
    4950  implements CollectionTransformer<I, I>
  • trunk/src/core/net/sf/basedb/util/biomaterial/SampleToBioSourceTransformer.java

    r5663 r6758  
    5353  @base.modified $Date$
    5454*/
     55@Deprecated
    5556public class SampleToBioSourceTransformer
    5657  implements CollectionTransformer<Sample, BioSource>
  • trunk/src/core/net/sf/basedb/util/biomaterial/SampleToExtractTransformer.java

    r5663 r6758  
    5252  @base.modified $Date$
    5353*/
     54@Deprecated
    5455public class SampleToExtractTransformer
    5556  implements CollectionTransformer<Sample, Extract>
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r6757 r6758  
    365365        for (Item item : Metadata.getAnnotatableItems())
    366366        {
    367           if (item.getDefinedPermissions() != null && item != Item.BIOMATERIALLIST)
     367          if (item.getDefinedPermissions() != null)
    368368          {
    369369            tmp.add(new GuiContext(item, GuiContext.Type.LIST));
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