Changeset 7121


Ignore:
Timestamp:
Apr 19, 2016, 8:56:43 AM (5 years ago)
Author:
Nicklas Nordborg
Message:

References #2000: Batch API for annotation handling

First version of the new AnnotationBatcher implementation. It should have support for creating, updating and deleting annotation values.

It lacks a lot functionality:

  • It doesn't check annotation values (eg. if a String is a String, if a values is allowed by the an enumerated annotation, etc.)
  • It doesn't handle units
  • Changes are not recorded in the change log


The AnnotationFlatFileImporter has been modified to use the batcher. All possible options for updating are supported (eg. merge).

Location:
trunk
Files:
1 added
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/config/dist/mysql-queries.xml

    r6981 r7121  
    3838  </query>
    3939
     40  <query id="AB_INSERT_INTO_ANNOTATIONS" type="SQL">
     41    <sql>
     42      INSERT INTO [Annotations] ([version], [annotationset_id], [annotationtype_id], [unit_id], [value_id], [last_update], [source])
     43      VALUES (0, ?, ?, ?, ?, ?, 0)
     44    </sql>
     45    <description>
     46      SQL query for inserting rows into the Annotations table.
     47      The primary key (id) must be auto-generated.
     48      Parameters: annotationset_id, annotationtype_id, unit_id, value_id, last_updated
     49    </description>
     50  </query>
     51 
     52  <query id="AB_INSERT_INTO_ANNOTATIONSETS" type="SQL">
     53    <sql>
     54      INSERT INTO [AnnotationSets] ([version], [item_type], [item_id])
     55      VALUES (0, {1}, ?)
     56    </sql>
     57    <description>
     58      SQL query for inserting rows into the AnnotationSets table.
     59      The primary key (id) must be auto-generated.
     60      Parameters: item_id
     61    </description>
     62  </query>
     63 
     64
     65
    4066</predefined-queries>
  • trunk/src/core/common-queries.xml

    r7082 r7121  
    35823582  </query>
    35833583
     3584  <query id="AB_LOAD_ANNOTATION_INFO" type="SQL">
     3585    <sql>
     3586      SELECT [annotationtype_id], [id], [version], [unit_id], [value_id], [last_update]
     3587      FROM [Annotations]
     3588      WHERE [annotationset_id] = :annotationSet AND [source] = 0
     3589    </sql>
     3590    <description>
     3591      SQL query for loading current (primary) annotations for
     3592      a given item.
     3593      Used by the AnnotationBatcher as a SQL query via Hibernate.
     3594    </description>
     3595  </query>
     3596
     3597  <query id="AB_LOAD_ANNOTATION_VALUES" type="SQL">
     3598    <sql>
     3599      SELECT [id], [value]
     3600      FROM [{1}]
     3601      WHERE [id] IN (:listOfIds)
     3602    </sql>
     3603    <description>
     3604      SQL query for loading current annotation values
     3605      for a given list of annotation value IDs.
     3606      Used by the AnnotationBatcher as a SQL query via Hibernate.
     3607    </description>
     3608  </query>
     3609
     3610  <query id="AB_INSERT_INTO_PARAMETERVALUES" type="SQL">
     3611    <sql>
     3612      INSERT INTO [ParameterValues] ([id], [discriminator], [version])
     3613      VALUES (nextval('hibernate_sequence'), ?, 0)
     3614    </sql>
     3615    <description>
     3616      SQL query for inserting rows into the ParameterValues table.
     3617      The primary key (id) must be auto-generated.
     3618      Parameters: discriminator
     3619    </description>
     3620  </query>
     3621
     3622  <query id="AB_INSERT_INTO_ANNOTATIONS" type="SQL">
     3623    <sql>
     3624      INSERT INTO [Annotations] ([id], [version], [annotationset_id], [annotationtype_id], [unit_id], [value_id], [last_update], [source])
     3625      VALUES (nextval('hibernate_sequence'), 0, ?, ?, ?, ?, ?, 0)
     3626    </sql>
     3627    <description>
     3628      SQL query for inserting rows into the Annotations table.
     3629      The primary key (id) must be auto-generated.
     3630      Parameters: annotationset_id, annotationtype_id, unit_id, value_id, last_updated
     3631    </description>
     3632  </query>
     3633
     3634  <query id="AB_UPDATE_ANNOTATIONS" type="SQL">
     3635    <sql>
     3636      UPDATE [Annotations]
     3637      SET [version] = ?, [unit_id] = ?, [last_update] = ?
     3638      WHERE [id] = ? AND [version] = ?
     3639    </sql>
     3640    <description>
     3641      SQL query for updating rows into the Annotations table.
     3642      Parameters: version (new), unit_id, last_updated, id, version (old)
     3643    </description>
     3644  </query>
     3645
     3646  <query id="AB_INSERT_INTO_ANNOTATIONSETS" type="SQL">
     3647    <sql>
     3648      INSERT INTO [AnnotationSets] ([id], [version], [item_type], [item_id])
     3649      VALUES (nextval('hibernate_sequence'), 0, {1}, ?)
     3650    </sql>
     3651    <description>
     3652      SQL query for inserting rows into the AnnotationSets table.
     3653      The primary key (id) must be auto-generated.
     3654      Parameters: item_id
     3655    </description>
     3656  </query>
     3657 
     3658  <query id="AB_UPDATE_ITEMTABLE" type="SQL">
     3659    <sql>
     3660      UPDATE [{1}]
     3661      SET [annotationset_id] = ?
     3662      WHERE [id] = ?
     3663    </sql>
     3664    <description>
     3665      SQL query for updating the annotationset_id column in any
     3666      table it exists in.
     3667      Parameters: annotationset_id, item_id
     3668    </description>
     3669  </query>
     3670
     3671  <query id="AB_NULLIFY_CLONED_ANNOTATIONS" type="SQL">
     3672    <sql>
     3673      UPDATE [Annotations]
     3674      SET [inherited_id] = null
     3675      WHERE [inherited_id] = ? and [source] = 2
     3676    </sql>
     3677    <description>
     3678      SQL query for setting the 'inherited_id' column to null
     3679      for cloned annotations that reference the annotation that
     3680      is about to be deleted.
     3681      Parameters: inherited_id
     3682    </description>
     3683  </query>
     3684
     3685  <query id="AB_DELETE_INHERITED_ANNOTATIONS" type="SQL">
     3686    <sql>
     3687      DELETE FROM [Annotations]
     3688      WHERE [inherited_id] = ? and [source] = 1
     3689    </sql>
     3690    <description>
     3691      SQL query for deleting inherited annotations that reference
     3692      the annotation that is about to be deleted.
     3693      Parameters: inherited_id
     3694    </description>
     3695  </query>
     3696
     3697  <query id="AB_DELETE_FROM_ANNOTATIONS" type="SQL">
     3698    <sql>
     3699      DELETE FROM [Annotations]
     3700      WHERE [id] = ?
     3701    </sql>
     3702    <description>
     3703      SQL query for deleting an annotation with a given id.
     3704      Used by the AnnotationBatcher as a PreparedStatement.
     3705      Parameters: id
     3706    </description>
     3707  </query>
     3708
     3709  <query id="AB_DELETE_FROM_PARAMETERVALUES" type="SQL">
     3710    <sql>
     3711      DELETE FROM [ParameterValues] WHERE [id] = ?
     3712    </sql>
     3713    <description>
     3714      SQL query for deleting a parameter value with a given id.
     3715      Used by the AnnotationBatcher as a PreparedStatement.
     3716    </description>
     3717  </query>
     3718
     3719  <query id="AB_DELETE_FROM_VALUES" type="SQL">
     3720    <sql>
     3721      DELETE FROM [{1}] WHERE [id] = ?
     3722    </sql>
     3723    <description>
     3724      SQL query for deleting all actual annotation values with a given id.
     3725      The {1} parameter is the table the value are stored in, eg. StringValues,
     3726      IntegerValues, FloatValues, etc.
     3727      Used by the AnnotationBatcher as a PreparedStatement.
     3728    </description>
     3729  </query>
     3730 
     3731  <query id="AB_INSERT_INTO_VALUES" type="SQL">
     3732    <sql>
     3733      INSERT INTO [{1}] ([id], [value]) VALUES (?, ?)
     3734    </sql>
     3735    <description>
     3736      SQL query for inserting annotation values in their respective
     3737      table (eg. StringValues, IntegerValues, FloatValues, etc.).
     3738      Used by the AnnotationBatcher as a PreparedStatement.
     3739    </description>
     3740  </query>
    35843741 
    35853742</predefined-queries>
  • trunk/src/core/net/sf/basedb/core/BasicItem.java

    r7082 r7121  
    281281  {
    282282    return 0;
     283  }
     284 
     285  private boolean hasBeenCalledFromGetAnnotationSet = false;
     286  private boolean hasBeenCalledFromAnnotationBatcher = false;
     287 
     288  /**
     289    Annotatable items that are used with the {@link AnnotationBatcher}
     290    must not call {@link Annotatable#getAnnotationSet()} in the same
     291    transaction. This method is a helper method for keeping track of
     292    which method that has been called.
     293    @param annotationSet TRUE when called from the getAnnotationSet method
     294    @param batcher TRUE when called from the batcher
     295    @since 3.8
     296  */
     297  void checkBatchAnnotatableUsage(boolean annotationSet, boolean batcher)
     298  {
     299    if (annotationSet)
     300    {
     301      if (hasBeenCalledFromAnnotationBatcher)
     302      {
     303        throw new IllegalStateException("Can't call getAnnotationSet() after the item has been used with an AnnotationBatcher: " + this);
     304      }
     305      hasBeenCalledFromGetAnnotationSet = true;
     306    }
     307    if (batcher)
     308    {
     309      if (hasBeenCalledFromGetAnnotationSet)
     310      {
     311        throw new IllegalStateException("Can't use with AnnotationBatcher after getAnnotationSet() has been called: " + this);
     312      }
     313      if (hasBeenCalledFromAnnotationBatcher)
     314      {
     315        throw new IllegalStateException("Can't use an item more than once with an AnnotationBatcher: " + this);
     316      }
     317      hasBeenCalledFromAnnotationBatcher = true;
     318    }
    283319  }
    284320 
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r7120 r7121  
    4242import net.sf.basedb.core.Annotatable;
    4343import net.sf.basedb.core.Annotation;
     44import net.sf.basedb.core.AnnotationBatcher;
     45import net.sf.basedb.core.AnnotationBatcher.Change;
    4446import net.sf.basedb.core.AnnotationSet;
    4547import net.sf.basedb.core.AnnotationType;
     
    594596  private List<String> columnHeaders;
    595597  private DbControl dc;
     598  private AnnotationBatcher batcher;
     599 
    596600  private UnitCache unitCache;
    597601  private FlatFileParser ffp;
     
    746750      ++i;
    747751    }
     752    batcher = new AnnotationBatcher(dc, itemType);
     753    batcher.addAnnotationTypes(mappers.values());
    748754   
    749755    // Include options
     
    946952          for (NewAnnotations na : n)
    947953          {
    948             na.setNewAnnotations(addToUnlimited, replaceExisting, failIfTooManyValues, removeExisting);
     954            na.setNewAnnotations(batcher, addToUnlimited, replaceExisting, failIfTooManyValues, removeExisting);
    949955            if (na.getNumSet() == 0) numItems--;
    950956            numAnnotations += na.getNumSet();
     
    961967
    962968        }
     969        batcher.close();
    963970        System.out.println(new Date()+": commit start");
    964971        dc.commit();
    965972        System.out.println(new Date()+": commit end");
    966973        if (progress != null) progress.display(100, "Done");
     974        //if (true) throw new RuntimeException("success!!");
    967975      }
    968976    }
     
    13761384        the multiplicity settings allows, TRUE to throw an exception
    13771385    */
    1378     void setNewAnnotations(boolean addToUnlimited, boolean replaceExisting,
     1386    void setNewAnnotations(AnnotationBatcher batcher, boolean addToUnlimited, boolean replaceExisting,
    13791387      boolean failIfTooManyValues, boolean removeAnnotations)
    13801388    {
    13811389      if (values.size() == 0) return;
    13821390      int numAnnotations = 0;
    1383       AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
     1391//      AnnotationSet as = item.isAnnotated() ? item.getAnnotationSet() : null;
     1392     
     1393      batcher.setCurrentItem(item);
     1394     
    13841395      for (Map.Entry<AnnotationType, List<AnnotationValue>> entry : values.entrySet())
    13851396      {
    13861397        AnnotationType at = entry.getKey();
    13871398        List<AnnotationValue> newValues = entry.getValue();
     1399       
     1400        List<Object> theValues = new ArrayList<Object>(newValues.size());
     1401        for (AnnotationValue value : newValues)
     1402        {
     1403          Object theValue = value.value;
     1404          theValues.add(theValue);
     1405        }
     1406        Change change = batcher.setValues(at, theValues, null);
     1407        if (change == Change.DELETED)
     1408        {
     1409          numRemoved++;
     1410        }
     1411        else if (change == Change.ADDED )
     1412        {
     1413          numSet += theValues.size();
     1414        }
     1415        else if (change == Change.UPDATED)
     1416        {
     1417          numSet += theValues.size();
     1418          numReplaced += theValues.size();
     1419        }
     1420       
     1421        /*
    13881422        int size = newValues.size();
    13891423        int multiplicity = at.getMultiplicity();
     
    14361470          }
    14371471        }
     1472        */
    14381473      }
    14391474    }
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