Changeset 7638

Timestamp:

Mar 11, 2019, 12:51:33 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #2136: Remove support for spot images

Removed things related to spot images from the BASE core. The schema update will drop the "SpotImages?" table.

Location:

trunk/src

Files:

• clients/web/net/sf/basedb/clients/web/PermissionUtil.java (modified) (2 diffs)
• clients/web/net/sf/basedb/clients/web/formatter/SpotImageFormatter.java (deleted)
• core/common-queries.xml (modified) (1 diff)
• core/net/sf/basedb/core/File.java (modified) (3 diffs)
• core/net/sf/basedb/core/Install.java (modified) (1 diff)
• core/net/sf/basedb/core/Item.java (modified) (1 diff)
• core/net/sf/basedb/core/RawBioAssay.java (modified) (2 diffs)
• core/net/sf/basedb/core/SpotImage.java (deleted)
• core/net/sf/basedb/core/SpotImages.java (deleted)
• core/net/sf/basedb/core/Update.java (modified) (2 diffs)
• core/net/sf/basedb/core/data/RawBioAssayData.java (modified) (1 diff)
• core/net/sf/basedb/core/data/SpotImagesData.java (deleted)

trunk/src/clients/web/net/sf/basedb/clients/web/PermissionUtil.java

@@ -162 +162 @@
     All items which permissions depend on some other item only.
   */
-  @SuppressWarnings("deprecation")
   private static final Set<Item> ignored = EnumSet.of(
     Item.SYSTEM, Item.HELP, 
@@ -170 +169 @@
     Item.PLATEEVENT, Item.PLATEEVENTTYPE, Item.WELL,
     Item.ARRAYDESIGNBLOCK, Item.FEATURE, Item.ARRAYDESIGNPLATE,
-    Item.SPOTIMAGES, Item.RAWDATA, 
+    Item.RAWDATA, 
     Item.BIOASSAYSET, Item.BIOASSAY, Item.TRANSFORMATION, Item.EXTRAVALUE,
     Item.VIRTUALDB, Item.DATACUBE, Item.DATACUBELAYER, Item.DATACUBECOLUMN, Item.DATACUBEFILTER,

trunk/src/core/common-queries.xml

@@ -925 +925 @@
   </query>
 
-  <query id="GET_SPOTIMAGES_FOR_FILE" type="HQL">
-    <sql>
-      SELECT {1}
-      FROM SpotImagesData spi
-      WHERE spi.redImageFile = :file 
-      OR spi.greenImageFile = :file 
-      OR spi.blueImageFile = :file 
-      OR spi.spotImagesFile = :file 
-    </sql>
-    <description>
-      A Hibernate query that gets spot images where a given 
-      file is used as one of the color components or holds the generated spot images.
-    </description>
-  </query>
-  
   <query id="GET_FILESETMEMBERS_FOR_FILE" type="HQL">
     <sql>

trunk/src/core/net/sf/basedb/core/File.java

@@ -550 +550 @@
       used = HibernateUtil.loadData(query2) > 0;
     }
-    if (!used)
-    {
-      org.hibernate.query.Query<Long> query2 = HibernateUtil.getPredefinedQuery(session, 
-        "GET_SPOTIMAGES_FOR_FILE", Long.class, "count(*)");
-      /*
-        SELECT {1}
-        FROM SpotImagesData spi
-        WHERE spi.redImageFile = :file 
-        OR spi.greenImageFile = :file 
-        OR spi.blueImageFile = :file 
-        OR spi.spotImagesFile = :file 
-      */
-      query2.setParameter("file", getId(), TypeWrapper.H_INTEGER);
-      used = HibernateUtil.loadData(query2) > 0;
-    }
     return used || super.isUsed();
   }
@@ -571 +556 @@
     <ul>
     <li>{@link FileAttachable} items with this file attached
-    <li>{@link SpotImages} using this file
     </ul>
     @since 2.2
   */
-  @SuppressWarnings("deprecation")
   @Override
   public Set<ItemProxy> getUsingItems()
@@ -616 +599 @@
     }   
     
-    // SpotImages
-    org.hibernate.query.Query<Integer> query3 = HibernateUtil.getPredefinedQuery(session, 
-      "GET_SPOTIMAGES_FOR_FILE", Integer.class, "spi.id");
-      /*
-        SELECT {1}
-        FROM SpotImagesData spi
-        WHERE spi.redImageFile = :file 
-        OR spi.greenImageFile = :file 
-        OR spi.blueImageFile = :file 
-        OR spi.spotImagesFile = :file 
-      */
-    query3.setParameter("file", getId(), TypeWrapper.H_INTEGER);
-    addUsingItems(using, Item.SPOTIMAGES, query3);
-
     return using;
   }

trunk/src/core/net/sf/basedb/core/Install.java

@@ -119 +119 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(145).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(147).intValue();
   
   public static synchronized int createTables(SchemaGenerator.Mode mode, ProgressReporter progress,

trunk/src/core/net/sf/basedb/core/Item.java

@@ -503 +503 @@
     300),
     
-  /**
-    The item is a {@link SpotImages}.
-    @deprecated In 3.14, will be removed in the future without replacement
-  */
-  @Deprecated
-  SPOTIMAGES(265, "Spot images", "spi", SpotImages.class, SpotImagesData.class, null,
-    310),
   /**
     The item is a {@link RawData} spot.

trunk/src/core/net/sf/basedb/core/RawBioAssay.java

@@ -31 +31 @@
 import net.sf.basedb.core.data.ReporterData;
 import net.sf.basedb.core.data.SoftwareData;
-import net.sf.basedb.core.data.SpotImagesData;
 import net.sf.basedb.core.hibernate.TypeWrapper;
 import net.sf.basedb.core.query.Restrictions;
@@ -924 +923 @@
   }
   
-  /**
-    Get the {@link SpotImages} item used to generate spot images
-    for this raw bioassay. If no <code>SpotImages</code> exists
-    a new one is created, and is automatically saved to the database (if 
-    commit is called).
-
-    @return The <code>SpotImages</code> item
-    @throws PermissionDeniedException If logged in user doesn't have read permission to the spot images. 
-    @throws BaseException If there is some kind of error.
-    @see #hasSpotImages()
-    @deprecated In 3.14, will be removed in the future without replacement
-  */
-  @Deprecated
-  public SpotImages getSpotImages()
-    throws PermissionDeniedException, BaseException
-  {
-    SpotImagesData spi = getData().getSpotImages();
-    SpotImages spotImages = null;
-    if (spi == null)
-    {
-      spotImages = SpotImages.getNew(getDbControl(), this);
-      getDbControl().saveItemIf(this, spotImages, false);
-    }
-    else
-    {
-      spotImages = getDbControl().getItem(SpotImages.class, spi);
-    }
-    return spotImages;
-  }
-  
-  /**
-    Check if spot images exists for this raw bioassay or not.
-    @see #getSpotImages()
-    @deprecated In 3.14, will be removed in the future without replacement
-  */
-  @Deprecated
-  public boolean hasSpotImages()
-  {
-    return getData().getSpotImages() != null;
-  }
-
   /**
     Get the value for the raw data header with the specified name.

trunk/src/core/net/sf/basedb/core/Update.java

@@ -704 +704 @@
       }
       
-      if (schemaVersion < 146)
-      {
-        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 146...");
-        schemaVersion = updateToSchemaVersion146(session, schemaVersion);
+      if (schemaVersion < 147)
+      {
+        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 147...");
+        schemaVersion = updateToSchemaVersion147(session, schemaVersion);
         progress_current += progress_step;
       }
@@ -2189 +2189 @@
   /**
     
-    @return The new schema version (=146)
+    @return The new schema version (=147)
   */
-  private static int updateToSchemaVersion146(org.hibernate.Session session, int currentSchemaVersion)
+  private static int updateToSchemaVersion147(org.hibernate.Session session, int currentSchemaVersion)
     throws BaseException
   {
-    final int schemaVersion = 146;
-    org.hibernate.Transaction tx = null;
-    
-    try
-    {
-      tx = HibernateUtil.newTransaction(session);
-
-      org.hibernate.query.Query<?> query = HibernateUtil.createQuery(session, 
-        "UPDATE PluginDefinitionData " + 
-        "SET disabled = true, name = CONCAT(name, ' (deprecated)') " +
-        "WHERE className='net.sf.basedb.plugins.SpotImageCreator'");
-      query.executeUpdate();
+    final int schemaVersion = 147;
+    try
+    {
+      
+      if (currentSchemaVersion < 146)
+      {
+        // First step is to update existing information
+        org.hibernate.Transaction tx = null;
+        try
+        {
+          tx = HibernateUtil.newTransaction(session);
+          
+          org.hibernate.query.Query<?> query = HibernateUtil.createQuery(session, 
+              "UPDATE PluginDefinitionData " + 
+              "SET disabled = true, name = CONCAT(name, ' (deprecated)') " +
+              "WHERE className='net.sf.basedb.plugins.SpotImageCreator'");
+            query.executeUpdate();
+          
+          setSchemaVersion(session, 146);
+          
+          // Commit the changes
+          HibernateUtil.commit(tx);
+        }
+        finally
+        {
+          if (tx != null && tx.getStatus() != TransactionStatus.COMMITTED) HibernateUtil.rollback(tx);
+        }
+      }
+
+      // Drop the 'SpotImages' table
+      dropTable(session, "SpotImages");
       
       // Update the schema version number
-//      setSchemaVersionInTransaction(session, schemaVersion);
-  
-      // Commit the changes
-      HibernateUtil.commit(tx);
-      log.info("updateToSchemaVersion146: OK");
+      setSchemaVersionInTransaction(session, schemaVersion);
+
+      log.info("updateToSchemaVersion147: OK");
     }
     catch (RuntimeException ex)
     {
-      if (tx != null) HibernateUtil.rollback(tx); 
-      log.error("updateToSchemaVersion146: FAILED", ex);
+      log.error("updateToSchemaVersion147: FAILED", ex);
       throw ex;
     }
     return schemaVersion;
-    
   }
 

trunk/src/core/net/sf/basedb/core/data/RawBioAssayData.java

@@ -189 +189 @@
   }
   
-  private SpotImagesData spotImages;
-  /**
-    Get the settings used for generating spot images for this raw bio assay.
-    @hibernate.one-to-one property-ref="rawBioAssay" cascade="delete"
-  */
-  public SpotImagesData getSpotImages()
-  {
-    return spotImages;
-  }
-  void setSpotImages(SpotImagesData spotImages)
-  {
-    this.spotImages = spotImages;
-  }
-  
   private DerivedBioAssayData bioAssay;
   /**