Changeset 7150


Ignore:
Timestamp:
Apr 27, 2016, 8:38:21 AM (6 years ago)
Author:
Nicklas Nordborg
Message:

Merge pre-3.8 changes to the trunk.

Location:
trunk
Files:
17 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/doc/src/docbook/admin/installation.xml

    r7079 r7150  
    5151        This section list some important information that may or may not
    5252        apply when upgrading from the <emphasis>previous</emphasis> BASE
    53         release to the current release (eg. 3.7 to 3.7). If you are
     53        release to the current release (eg. 3.7 to 3.8). If you are
    5454        upgrading from a BASE installation that is older (3.0-3.6)
    5555        you should also read <xref linkend="appendix.update_warnings" />.
  • trunk/src/core/net/sf/basedb/core/AnnotationBatcher.java

    r7134 r7150  
    7272  <li>The batcher only works with {@link Annotation.Source#PRIMARY} annotations.
    7373 
    74   <li>The {@link #setValues(AnnotationType, List, Unit)} can only be called once
     74  <li>The {@link #setValues(AnnotationType, List, Unit, boolean)} can only be called once
    7575    per item and annotation type.
    76  
    77   <li>More... ??
    7876 
    7977  </ul>
     
    579577  /**
    580578    Add, update or delete a single-valued annotation.
    581     See {@link #setValues(AnnotationType, List, Unit)} for
     579    See {@link #setValues(AnnotationType, List, Unit, boolean)} for
    582580    more information.
    583581  */
     
    610608    the enumeration, within bounds of min and max values, etc.)
    611609
    612     @param at The annotation type, which must be one of the annotation types
     610    @param annotationType The annotation type, which must be one of the annotation types
    613611      specified when creating the batcher
    614612    @param values The values to set or null/empty to remove values
     
    616614    @param merge If TRUE and the annotation type allows an unlimted number
    617615      of annotations (multiplicity=0) merges the new values with the existing values.
    618       Ignored if multiplicity > 0.
     616      Ignored if multiplicity &gt; 0.
    619617   
    620618    @return The resulting change
     
    821819    A flag indicating what type of change that was made to an
    822820    annotation as a result of calling
    823     {@link AnnotationBatcher#setValues(AnnotationType, List, Unit)}
     821    {@link AnnotationBatcher#setValues(AnnotationType, List, Unit, boolean)}
    824822  */
    825823  public static enum Change
  • trunk/src/core/net/sf/basedb/core/ExtendedPropertyAccessor.java

    r7075 r7150  
    4747  and <code>Setter</code> objects for each extended property of an
    4848  <code>Extendable</code> item. These objects are then used to access the
    49   extended properties for all items via the {@link org.hibernate.property.Getter#get(Object)
    50   GetterSetter.get} and {@link org.hibernate.property.Setter#set(Object,Object,SessionFactoryImplementor)
     49  extended properties for all items via the {@link Getter#get(Object)
     50  GetterSetter.get} and {@link Setter#set(Object,Object,SessionFactoryImplementor)
    5151  GetterSetter.set} methods.
    5252
  • trunk/src/core/net/sf/basedb/core/HibernateUtil.java

    r7075 r7150  
    23472347   
    23482348    /**
    2349       Clone the <filter-def> with the given name and insert
    2350       a new item-specific <filter-def> definition into the
    2351       document given by the <class> element.
     2349      Clone the &lt;filter-def&gt; with the given name and insert
     2350      a new item-specific &lt;filter-def&gt; definition into the
     2351      document given by the &lt;class&gt; element.
    23522352    */
    23532353    void createItemSpecificFilterDef(String name, Item itemType, Element classTag)
     
    23612361 
    23622362    /**
    2363       Generic filters can be added as <filter> elements in the
     2363      Generic filters can be added as &lt;filter&lt; elements in the
    23642364      mapping file.
    23652365    */
     
    23752375      Item-specific filters are stored internally and registered later
    23762376      by {@link #registerDelayedFilters(org.hibernate.boot.Metadata)}.
    2377       We need to do this since a <filter> tag is not allowed
    2378       for items defined with <subclass>. Programmatically we can add
     2377      We need to do this since a &lt;filter&gt; tag is not allowed
     2378      for items defined with &lt;subclass&gt;. Programmatically we can add
    23792379      the filter later but not until the configuration process has
    23802380      gone far enough so that we have access to PersistentClass instances.
  • trunk/src/core/net/sf/basedb/core/ServiceSessionControl.java

    r7075 r7150  
    103103    <p>
    104104    If you want to use connections/transactions that are independent from BASE
    105     call {@link #useSeparateConnections()} but make sure you also get connection
    106     pooling configured. You can still use "piggy-backed" connections.
    107 
     105    call {@link SessionFactoryConfiguration#setUseSeparateConnections(boolean)}
     106    but make sure you also get connection pooling configured.
     107    You can still use "piggy-backed" connections.
    108108   
    109109    @param appId The ID of the extensions (which should be unique)
    110110    @param schema  The schema name the extension wants to use for it's database tables
    111     @param schemaVersion
    112     @param classLoader
    113     @return
     111    @param schemaVersion The version of the current schema. If this is different from the
     112      database scheme it will automatically be updated when {@link #buildSessionFactory(SessionFactoryConfiguration)}
     113      is called.
     114    @param classLoader A class loader is needed for Hibernate to be able to locate the
     115      classes. Use the classloader returned from {@link Class#getClassLoader()} using the
     116      class from one of the classes in the extension
    114117  */
    115118  public SessionFactoryConfiguration createSessionFactoryConfiguration(String appId, String schema, int schemaVersion, ClassLoader classLoader)
  • trunk/src/core/net/sf/basedb/core/data/AnnotatedData.java

    r6127 r7150  
    6161    this.annotationSet = annotationSet;
    6262  }
     63  private Set<AnnotationLink> links;
    6364  @Override
    6465  public Set<AnnotationLink> getAnnotations()
    6566  {
    66     return null;
     67    return links;
    6768  }
    6869  void setAnnotations(Set<AnnotationLink> links)
    69   {}
     70  {
     71    this.links = links;
     72  }
    7073  // -------------------------------------------
    7174 
  • trunk/src/core/net/sf/basedb/core/data/BioAssayData.java

    r6468 r7150  
    9696    this.annotationSet = annotationSet;
    9797  }
     98  private Set<AnnotationLink> links;
    9899  @Override
    99100  public Set<AnnotationLink> getAnnotations()
    100101  {
    101     return null;
    102   }
    103   void setAnnotations(Set<AnnotationLink> annotations)
    104   {}
     102    return links;
     103  }
     104  void setAnnotations(Set<AnnotationLink> links)
     105  {
     106    this.links = links;
     107  }
    105108  // -------------------------------------------
    106109
  • trunk/src/core/net/sf/basedb/core/data/BioAssaySetData.java

    r7015 r7150  
    113113    this.annotationSet = annotationSet;
    114114  }
     115  private Set<AnnotationLink> links;
    115116  @Override
    116117  public Set<AnnotationLink> getAnnotations()
    117118  {
    118     return null;
    119   }
    120   void setAnnotations(Set<AnnotationLink> annotations)
    121   {}
     119    return links;
     120  }
     121  void setAnnotations(Set<AnnotationLink> links)
     122  {
     123    this.links = links;
     124  }
    122125  // -------------------------------------------
    123126  /*
  • trunk/src/core/net/sf/basedb/core/data/PluginDefinitionData.java

    r7015 r7150  
    8080    this.annotationSet = annotationSet;
    8181  }
     82  private Set<AnnotationLink> links;
    8283  @Override
    8384  public Set<AnnotationLink> getAnnotations()
    8485  {
    85     return null;
    86   }
    87   void setAnnotations(Set<AnnotationLink> annotations)
    88   {}
     86    return links;
     87  }
     88  void setAnnotations(Set<AnnotationLink> links)
     89  {
     90    this.links = links;
     91  }
    8992  // -------------------------------------------
    9093  /*
  • trunk/src/core/net/sf/basedb/core/data/RootRawBioAssayData.java

    r6915 r7150  
    5858    this.annotationSet = annotationSet;
    5959  }
     60  private Set<AnnotationLink> links;
    6061  @Override
    6162  public Set<AnnotationLink> getAnnotations()
    6263  {
    63     return null;
     64    return links;
    6465  }
    65   void setAnnotations(Set<AnnotationLink> annotations)
    66   {}
     66  void setAnnotations(Set<AnnotationLink> links)
     67  {
     68    this.links = links;
     69  }
    6770  // -------------------------------------------
    6871  /*
  • trunk/src/core/net/sf/basedb/core/data/WellData.java

    r6127 r7150  
    6060    this.annotationSet = annotationSet;
    6161  }
     62  private Set<AnnotationLink> links;
    6263  @Override
    6364  public Set<AnnotationLink> getAnnotations()
    6465  {
    65     return null;
     66    return links;
    6667  }
    67   void setAnnotations(Set<AnnotationLink> annotations)
    68   {}
     68  void setAnnotations(Set<AnnotationLink> links)
     69  {
     70    this.links = links;
     71  }
    6972  // -------------------------------------------
    7073 
  • trunk/src/core/net/sf/basedb/core/hibernate/SchemaGenerator.java

    r7075 r7150  
    8383    Create a new schema generator.
    8484   
    85     @param cfg The current configuration
     85    @param metadata Information about current configuration
    8686    @param dialect The dialect of the database we are connecting to
    8787    @param dbEngine The DbEngine for the database we are connecting to
  • trunk/src/core/net/sf/basedb/core/hibernate/SessionFactoryConfiguration.java

    r7075 r7150  
    3030  Class for holding configuration options for creating
    3131  extra session factories for services. Used by
    32   {@link ServiceSessionControl#buildSessionFactory(SessionFactoryConfiguration)}.
     32  ServiceSessionControl#buildSessionFactory(SessionFactoryConfiguration).
    3333  <p>
    3434  This class has been deprecated and can no longer be used for configuring session
     
    142142    Get the schema version that was installed prior to updating it.
    143143    Note that this value is only available after calling
    144     {@link ServiceSessionControl#buildSessionFactory(SessionFactoryConfiguration)}.
     144    ServiceSessionControl#buildSessionFactory(SessionFactoryConfiguration).
    145145  */
    146146  public int getInstalledSchemaVersion()
  • trunk/src/core/net/sf/basedb/util/formatter/EnumFormatter.java

    r7088 r7150  
    4848    @param enumClass Only required if using the parseString method
    4949    @param nullValue The string to return if a null item is
    50       passed to {@link #format(Integer)}
     50      passed to {@link #format(Enum)}
    5151  */
    5252  public EnumFormatter(Class<T> enumClass, String nullValue)
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r7129 r7150  
    14221422    /**
    14231423      Number of annotations that was set (=added or replaced) by the call to the
    1424       {@link #setNewAnnotations(boolean, boolean, boolean, boolean)} method.
     1424      {@link #setNewAnnotations(AnnotationBatcher, boolean, boolean, boolean, boolean)} method.
    14251425    */
    14261426    int getNumSet()
     
    14311431    /**
    14321432      Number of annotations that was replaced by the call to the
    1433       {@link #setNewAnnotations(boolean, boolean, boolean, boolean)} method.
     1433      {@link #setNewAnnotations(AnnotationBatcher, boolean, boolean, boolean, boolean)} method.
    14341434    */
    14351435    int getNumReplaced()
     
    14401440    /**
    14411441      Number of annotations that was removed by the call to the
    1442       {@link #setNewAnnotations(boolean, boolean, boolean, boolean)} method.
     1442      {@link #setNewAnnotations(AnnotationBatcher, boolean, boolean, boolean, boolean)} method.
    14431443      @since 2.8
    14441444    */
     
    14501450    /**
    14511451      Number of annotations that was couldn't be set by the call to the
    1452       {@link #setNewAnnotations(boolean, boolean, boolean, boolean)} method because of an
     1452      {@link #setNewAnnotations(AnnotationBatcher, boolean, boolean, boolean, boolean)} method because of an
    14531453      error (too many values).
    14541454    */
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AnnotationTypeImporter.java

    r7102 r7150  
    380380  }
    381381  /**
    382     Calls {@link AnnotationType#getQuery()}.
     382    Calls {@link AnnotationType#getQuery(Item)}.
    383383  */
    384384  @Override
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