Changeset 7642


Ignore:
Timestamp:
Mar 12, 2019, 7:53:27 AM (4 years ago)
Author:
Nicklas Nordborg
Message:

References #2137: Remove some of the deprecated code

Removed things that was deprecated a long time ago and that are not so likely to be used by plug-ins or extensions.

Location:
trunk/src
Files:
6 deleted
13 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/core/net/sf/basedb/core/DerivedBioAssay.java

    r7381 r7642  
    513513  // -------------------------------------------
    514514
    515   /**
    516     Get the physical bioassay that is the root bioassay for this derived
    517     bioassay set. This property is always inherited down to child events
    518     so this method never return null.
    519     @deprecated In 3.2, replaced with {@link #getPhysicalBioAssays()}.
    520     @return Always null
    521   */
    522   @Deprecated
    523   public PhysicalBioAssay getPhysicalBioAssay()
    524   {
    525     return null;
    526   }
    527  
    528515  public void testFixChildren()
    529516  {
    … …  
    594581  }
    595582
    596  
    597   /**
    598     Get the parent derived bioassay set.   
    599     @deprecated In 3.2, replaced with {@link #getParents()}
    600     @return Always null
    601   */
    602   @Deprecated
    603   public DerivedBioAssay getParent()
    604   {
    605     return null;
    606   }
    607 
    608  
    609583  /**
    610584    Add a derived bioassay as a parent to this derived bioassay.

  • trunk/src/core/net/sf/basedb/core/ItemContext.java

    r7610 r7642  
    17641764 
    17651765  /**
    1766     @deprecated In 3.1, use {@link #configureQuery(DbControl, SqlQuery, List)} instead
    1767   */
    1768   @Deprecated
    1769   public void configureQuery(DbControl dc, AbstractSqlQuery query, List<String> selectionList)
    1770   {
    1771     configureQuery(dc, (SqlQuery)query, selectionList);
    1772   }
    1773 
    1774   /**
    17751766    Use the settings in this context to configure a dynamic query.
    17761767    <ul>
    … …  
    19011892
    19021893  /**
    1903     @deprecated In 3.9.2, use {@link #getDynamicExpression(DbControl, SqlQuery, String)} instead
    1904   */
    1905   @Deprecated
    1906   public static Expression getDynamicExpression(DbControl dc, String propertyDef)
    1907   {
    1908     return getDynamicExpression(dc, null, propertyDef);
    1909   }
    1910 
    1911  
    1912   /**
    19131894    Create an {@link Expression} from a string. If the string starts with:
    19141895   
    … …  
    20181999 
    20192000  /**
    2020     @deprecated In 3.9.2, use {@link #getDynamicSelect(DbControl, SqlQuery, String)} instead
    2021   */
    2022   @Deprecated
    2023   public static Select getDynamicSelect(DbControl dc, String propertyDef)
    2024   {
    2025     return getDynamicSelect(dc, null, propertyDef);
    2026   }
    2027 
    2028   /**
    20292001    Same as {@link #getDynamicExpression(DbControl, String)} but generates
    20302002    a select object instead.

  • trunk/src/core/net/sf/basedb/core/PluginSessionControl.java

    r6437 r7642  
    6161    throw new PermissionDeniedException("login");
    6262  }
    63 
    64   /**
    65     @throws PermissionDeniedException Always
    66   */
    67   @Override
    68   @Deprecated
    69   public synchronized void login(String login, String password, String comment)
    70     throws ItemNotFoundException, PermissionDeniedException, InvalidPasswordException, BaseException
    71   {
    72     throw new PermissionDeniedException("login");
    73   }
    7463 
    7564  @Override

  • trunk/src/core/net/sf/basedb/core/PropertyFilter.java

    r7605 r7642  
    11041104
    11051105  /**
    1106     @deprecated In 3.9.2, use {@link #getDynamicRestriction(DbControl, SqlQuery)} instead
    1107   */
    1108   @Deprecated
    1109   public Restriction getDynamicRestriction(DbControl dc)
    1110   {
    1111     return getDynamicRestriction(dc, null);
    1112   }
    1113  
    1114   /**
    11151106    @since 3.9.2
    11161107  */

  • trunk/src/core/net/sf/basedb/core/SessionControl.java

    r7622 r7642  
    400400  }
    401401 
    402   /**
    403     @deprecated In 3.3, use {@link #login(LoginRequest)} instead
    404   */
    405   @Deprecated
    406   public synchronized void login(String login, String password, String comment)
    407   {
    408     LoginRequest loginRequest = new LoginRequest();
    409     loginRequest.setLogin(login);
    410     loginRequest.setPassword(password);
    411     loginRequest.setComment(comment);
    412     login(loginRequest);
    413   }
    414 
    415402  /**
    416403    Log in to BASE. The method checks that the given login is valid,

  • trunk/src/core/net/sf/basedb/core/VirtualTable.java

    r5888 r7642  
    8181      return allColumns;
    8282    }
    83    
    84     @Override
    85     @Deprecated
    86     public VirtualColumn[] getColumns(RawDataType rdt)
    87     {
    88       VirtualColumn[] columns = super.getColumns(rdt);
    89       VirtualColumn[] allColumns = new VirtualColumn[columns.length + rdt.getChannels()];
    90       System.arraycopy(columns, 0, allColumns, 0, columns.length);
    91       for (int i = 0; i < rdt.getChannels(); ++i)
    92       {
    93         allColumns[i+columns.length] = VirtualColumn.channelRaw(i+1);
    94       }
    95       return allColumns;
    96     }
     83
    9784  },
    9885 
    … …  
    278265    }
    279266   
    280     /**
    281       @throws UnsupportedOperationException Must use the non-deprecated methods
    282     */
    283     @Override
    284     @Deprecated
    285     public VirtualColumn[] getColumns(RawDataType rdt)
    286     {
    287       throw new UnsupportedOperationException("getColumns(RawDataType)");
    288     }
    289267
    290268    /**
    … …  
    371349  /**
    372350    Get all columns in this table.
    373     @param rdt The raw data type of the experiment
    374     @deprecated In 3.1, use {@link #getColumns(VirtualDb)} or
    375       {@link #getColumns(Experiment)} instead
    376   */
    377   @Deprecated
    378   public VirtualColumn[] getColumns(RawDataType rdt)
    379   {
    380     return Arrays.copyOf(columns, columns.length);
    381   }
    382  
    383   /**
    384     Get all columns in this table.
    385351    @param vdb The virtual database this table belongs to
    386352    @since 3.1
    … …  
    420386 
    421387  /**
    422     Get the number of bytes a single row in the database occupies.
    423     The number doesn't include any variable length columns, ie. string
    424     columns. The caller should add the string length to the value
    425     returned from this method.
    426     @param rdt The raw data type of the experiment
    427     @deprecated In 3.1, use {@link #getBytesPerRow(Experiment)}
    428       or {@link #getBytesPerRow(VirtualDb)} instead
    429   */
    430   @Deprecated
    431   public long getBytesPerRow(RawDataType rdt)
    432   {
    433     long bytesPerRow = 0;
    434     for (VirtualColumn vc : getColumns(rdt))
    435     {
    436       bytesPerRow += vc.getTypeWrapper().getApproximateSize();
    437     }
    438     return bytesPerRow;
    439   }
    440  
    441   /**
    442388    @see #getBytesPerRow(VirtualDb)
    443389    @since 3.1

  • trunk/src/core/net/sf/basedb/core/log/EntityDetails.java

    r6898 r7642  
    227227    }
    228228    return propertyIsDirty;
    229   }
    230  
    231   /**
    232     Create a new ChangeHistoryDetailData object from the information
    233     in this object assuming that the entity is a subclass of
    234     {@link BasicData}.
    235     @param detailedProperties If TRUE, the {@link ChangeHistoryDetailData#getChangeInfo()}
    236       is populated with a list of the names of the modified properties (only
    237       relevant for UPDATE changes)
    238     @return A new ChangeHistoryDetailData instance
    239     @deprecated In 3.3. Use {@link #toChangeDetails(boolean, boolean)} instead
    240   */
    241   @Deprecated
    242   public ChangeHistoryDetailData toChangeHistoryDetailData(boolean detailedProperties)
    243   {
    244     return toChangeHistoryDetailData((BasicData)entity, changeType, detailedProperties);
    245   }
    246 
    247   /**
    248     Create a new ChangeHistoryDetailData object using a mix of the information
    249     in this object, and the given parameters.
    250     @param data The entity that was changed
    251     @param changeType The change type
    252     @param detailedProperties If TRUE, the {@link ChangeHistoryDetailData#getChangeInfo()}
    253       is populated with a list of the names of the modified properties (only
    254       relevant for UPDATE changes)
    255     @return  A new ChangeHistoryDetailData instance
    256     @deprecated In 3.3. Use {@link #toChangeDetails(Item, int, String, ChangeType, boolean, boolean)} instead
    257   */
    258   @Deprecated
    259   public ChangeHistoryDetailData toChangeHistoryDetailData(BasicData data, ChangeType changeType, boolean detailedProperties)
    260   {
    261     ChangeHistoryDetailData details = new ChangeHistoryDetailData();
    262     details.setChangeType(changeType.getValue());
    263     details.setItemId(data.getId());
    264     details.setItemType(Item.fromDataObject(data).getValue());
    265     if (detailedProperties)
    266     {
    267       details.setChangeInfo(getModifiedProperties("Updated: ", ", ", null));
    268     }
    269     return details;
    270229  }
    271230 

  • trunk/src/core/net/sf/basedb/util/JarClassLoader.java

    r7622 r7642  
    146146  {
    147147    return new JarClassLoader(jarPath);
    148   }
    149  
    150  
    151   /**
    152     Unload the class loader for the given JAR file. The class loader will
    153     not be unloaded if the calling application has object references to the
    154     class loader or any class loaded by the class loader. However, if the
    155     {@link #getInstance(String)} method is called again, a new class loader
    156     instance will be created.
    157    
    158     @param jarPath The path to the JAR file
    159     @deprecated In 3.3.4, use {@link #newInstance(String)} or {@link #getInstance(String, boolean)} with autoUnload=true instead
    160   */
    161   @Deprecated
    162   public static final void unload(String jarPath)
    163   {
    164     synchronized (classLoaders)
    165     {
    166       classLoaders.remove(jarPath);
    167     }
    168148  }
    169149 

  • trunk/src/core/net/sf/basedb/util/extensions/Registry.java

    r7605 r7642  
    199199 
    200200  /**
    201     Note that this method uses the class loader from the 'eventHandler' as
    202     the third parameter!
    203     @since 2.8
    204     @deprecated In 3.10, use {@link #registerEventHandler(EventHandler, EventFilter, ClassLoader)} instead
    205   */
    206   @Deprecated
    207   public synchronized void registerEventHandler(EventHandler eventHandler, EventFilter filter)
    208   {
    209     if (eventHandler == null) return;
    210     registerEventHandler(eventHandler, filter, eventHandler.getClass().getClassLoader());
    211   }
    212  
    213   /**
    214201    Register an event handler for responding to events happening to
    215202    extension points and extensions in the registry. The registry itself
    … …  
    325312 
    326313  /**
    327     @deprecated In 3.2, use {@link #registerExtensionPoint(ExtensionPoint, ClassLoader)} instead
    328   */
    329   @Deprecated
    330   public synchronized <A extends Action> void
    331     registerExtensionPoint(ExtensionPoint<A> extensionPoint)
    332   {
    333     registerExtensionPoint(extensionPoint, null);
    334   }
    335  
    336   /**
    337314    Register an extension point. If the extension point already exists,
    338315    the description and renderer factory is updated. The action class
    … …  
    464441    RegisteredExtensionPoint<?> rep = extensionPoints.get(id);
    465442    return rep == null ? null : rep.getLastError();
    466   }
    467  
    468   /**
    469     @deprecated In 3.2, use {@link #registerExtension(Extension, ClassLoader)} instead
    470   */
    471   @Deprecated
    472   public synchronized <A extends Action> void registerExtension(Extension<A> extension)
    473   {
    474     registerExtension(extension, null);
    475443  }
    476444

  • trunk/src/core/net/sf/basedb/util/extensions/manager/processor/ExtractResourcesProcessor.java

    r6444 r7642  
    240240 
    241241  /**
    242     Set a flag indicating if already existing files should
    243     always be updated or not.
    244    
    245     @param forceOverwrite TRUE to force overwriting existing files,
    246       FALSE to only overwrite files if they are different from
    247       the files in the JAR
    248     @deprecated In 3.1, no replacement since all files must be overwritten to ensure
    249       proper functionality
    250   */
    251   @Deprecated
    252   public void setForceOverwrite(boolean forceOverwrite)
    253   {}
    254  
    255   /**
    256242    Get the number of files that was successfully processed.
    257243  */

  • trunk/src/core/net/sf/basedb/util/overview/OverviewUtil.java

    r7605 r7642  
    7373
    7474  /**
    75     @return Same as {@link #getStaticRules()}
    76     @deprecated In 3.2, use {@link #getStaticRules()} or {@link #getAllRules(DbControl, GenericOverview)} instead
    77   */
    78   @Deprecated
    79   public static Map<String, List<ValidationRuleAction>> getValidators()
    80   {
    81     return getStaticRules();
    82   }
    83 
    84   /**
    8575    Get all static (built-in) validation rules grouped by relationship. The key of the map
    8676    is a title that groups related validation rules, for example:

  • trunk/src/core/net/sf/basedb/util/overview/ValidationOptions.java

    r6047 r7642  
    7373  }
    7474 
    75   /**
    76     @deprecated In 3.2, use {@link #getSeverity(ValidationRuleAction)} instead
    77   */
    78   @Deprecated
    79   public Severity getSeverity(Validator validator)
    80   {
    81     return getSeverity((ValidationRuleAction)validator);
    82   }
    83  
     75
    8476  /**
    8577    Get the severity level for the specified validator rule. If no option
    … …  
    9789  }
    9890 
    99   /**
    100     @deprecated In 3.2, use {@link #setSeverity(ValidationRuleAction, Severity)} instead
    101   */
    102   @Deprecated
    103   public void setSeverity(Validator validator, Severity severity)
    104   {
    105     setSeverity((ValidationRuleAction)validator, severity);
    106   }
    107 
    10891  /**
    10992    Set a severity level for the specified validation rule.
    … …  
    124107  }
    125108
    126  
    127   /**
    128     @since 2.13
    129     @deprecated In 3.2, use {@link #getOption(ValidationRuleAction, String, String)} instead
    130   */
    131   @Deprecated
    132   public String getOption(Validator validator, String key, String defaultValue)
    133   {
    134     return getOption((ValidationRuleAction)validator, key, defaultValue);
    135   }
    136 
    137109  /**
    138110    Get the configured option for a validator rule.
    … …  
    149121    if (value == null) value = defaultValue;
    150122    return value;
    151   }
    152 
    153  
    154   /**
    155     @since 2.13
    156     @deprecated In 3.2, use {@link #setOption(ValidationRuleAction, String, String)} instead
    157   */
    158   @Deprecated
    159   public void setOption(Validator validator, String key, String value)
    160   {
    161     setOption((ValidationRuleAction)validator, key, value);
    162123  }
    163124

  • trunk/src/plugins/core/core-plugins.xml

    r7637 r7642  
    609609  </plugin-definition>
    610610
    611   <!-- Used for backwards compatibility with older server installations -->
    612   <plugin-definition id="LabeledExtractImporter">
    613     <about>
    614       <name>Labeled extract importer (deprecated)</name>
    615       <description>
    616         Imports and updates labeled extracts in a batch.
    617       </description>
    618     </about>
    619     <plugin-class>net.sf.basedb.plugins.batchimport.LabeledExtractImporter</plugin-class>
    620     <settings>
    621       <property name="everyone-use">1</property>
    622       <property name="deprecated">1</property>
    623     </settings>
    624   </plugin-definition>
    625 
    626   <!-- Used for backwards compatibility with older server installations -->
    627   <plugin-definition id="HybridizationImporter">
    628     <about>
    629       <name>Hybridization importer (deprecated)</name>
    630       <description>
    631         Imports and updates hybridizations in a batch.
    632       </description>
    633     </about>
    634     <plugin-class>net.sf.basedb.plugins.batchimport.HybridizationImporter</plugin-class>
    635     <settings>
    636       <property name="everyone-use">1</property>
    637       <property name="deprecated">1</property>
    638     </settings>
    639   </plugin-definition>
    640 
    641611  <plugin-definition id="PhysicalBioAssayImporter">
    642612    <about>
    … …  
    649619    <settings>
    650620      <property name="everyone-use">1</property>
    651     </settings>
    652   </plugin-definition>
    653  
    654   <!-- Used for backwards compatibility with older server installations -->
    655   <plugin-definition id="ScanImporter">
    656     <about>
    657       <name>Scan importer (deprecated)</name>
    658       <description>
    659         Imports and updates scans in a batch.
    660       </description>
    661     </about>
    662     <plugin-class>net.sf.basedb.plugins.batchimport.ScanImporter</plugin-class>
    663     <settings>
    664       <property name="everyone-use">1</property>
    665       <property name="deprecated">1</property>
    666621    </settings>
    667622  </plugin-definition>
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