Allow the PixelsService to be runtime configured

src/main/java/com/glencoesoftware/omero/ms/core/OmeroAmazonS3ClientFactory.java → src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java

@@ -15,7 +15,7 @@
  * with this program; if not, write to the Free Software Foundation, Inc.,
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
-package com.glencoesoftware.omero.ms.core;
+package com.glencoesoftware.omero.zarr;
 
 import java.net.URI;
 import java.util.HashMap;

src/main/java/com/glencoesoftware/omero/ms/core/OmeroS3FileSystem.java → src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java

@@ -15,7 +15,7 @@
  * with this program; if not, write to the Free Software Foundation, Inc.,
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
-package com.glencoesoftware.omero.ms.core;
+package com.glencoesoftware.omero.zarr;
 
 import java.io.IOException;
 

src/main/java/com/glencoesoftware/omero/ms/core/OmeroS3ReadOnlySeekableByteChannel.java → src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java

@@ -15,7 +15,7 @@
  * with this program; if not, write to the Free Software Foundation, Inc.,
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
-package com.glencoesoftware.omero.ms.core;
+package com.glencoesoftware.omero.zarr;
 
 
 import java.io.ByteArrayInputStream;

src/main/java/com/glencoesoftware/omero/ms/core/ZarrPixelBuffer.java → src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelBuffer.java

@@ -16,7 +16,7 @@
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
 
-package com.glencoesoftware.omero.ms.core;
+package com.glencoesoftware.omero.zarr;
 
 import java.awt.Dimension;
 import java.io.IOException;

src/main/java/com/glencoesoftware/omero/ms/core/PixelsService.java → src/main/java/com/glencoesoftware/omero/zarr/ZarrPixelsService.java

@@ -16,7 +16,7 @@
  * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  */
 
-package com.glencoesoftware.omero.ms.core;
+package com.glencoesoftware.omero.zarr;
 
 import java.io.File;
 import java.io.IOException;
@@ -58,10 +58,10 @@
  * @author Chris Allan <[email protected]>
  *
  */
-public class PixelsService extends ome.io.nio.PixelsService {
+public class ZarrPixelsService extends ome.io.nio.PixelsService {
 
     private static final org.slf4j.Logger log =
-            LoggerFactory.getLogger(PixelsService.class);
+            LoggerFactory.getLogger(ZarrPixelsService.class);
 
     public static final String NGFF_ENTITY_TYPE = "com.glencoesoftware.ngff:multiscales";
     public static final long NGFF_ENTITY_ID = 3;
@@ -85,7 +85,7 @@ public class PixelsService extends ome.io.nio.PixelsService {
     /** Array path vs. ZarrArray cache */
     private final AsyncLoadingCache<Path, ZarrArray> zarrArrayCache;
 
-    public PixelsService(
+    public ZarrPixelsService(
             String path, boolean isReadOnlyRepo, File memoizerDirectory,
             long memoizerWait, FilePathResolver resolver, BackOff backOff,
             TileSizes sizes, IQuery iQuery,
@@ -102,10 +102,10 @@ public PixelsService(
         this.iQuery = iQuery;
         zarrMetadataCache = Caffeine.newBuilder()
                 .maximumSize(this.zarrCacheSize)
-                .buildAsync(PixelsService::getZarrMetadata);
+                .buildAsync(ZarrPixelsService::getZarrMetadata);
         zarrArrayCache = Caffeine.newBuilder()
                 .maximumSize(this.zarrCacheSize)
-                .buildAsync(PixelsService::getZarrArray);
+                .buildAsync(ZarrPixelsService::getZarrArray);
     }
 
     /**
@@ -242,17 +242,35 @@ public String getUri(IObject object) {
     }
 
     /**
-     * Retrieve the {@link Image} for a particular set of pixels.
+     * Retrieve the {@link Image} for a particular set of pixels.  Where
+     * possible, does not initiate a query.
      * @param pixels Pixels set to retrieve the {@link Image} for.
      * @return See above.
      */
     protected Image getImage(Pixels pixels) {
         if (pixels.getImage().isLoaded()) {
+            // Will likely only be true when operating within a microservice
             return pixels.getImage();
         }
         return iQuery.get(Image.class, pixels.getImage().getId());
     }
 
+    /**
+     * Retrieves the series for a given set of pixels.  Where possible, does not
+     * initiate a query.
+     * @param pixels Set of pixels to return the series for.
+     * @return The series as specified by the pixels parameters or
+     * <code>0</code> (the first series).
+     */
+    @Override
+    protected int getSeries(Pixels pixels) {
+        if (pixels.getImage().isLoaded()) {
+            // Will likely only be true when operating within a microservice
+            return pixels.getImage().getSeries();
+        }
+        return super.getSeries(pixels);
+    }
+
     /**
      * Returns a label image NGFF pixel buffer if it exists.
      * @param mask Mask to retrieve a pixel buffer for.

src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java

@@ -35,9 +35,9 @@
 import java.util.Properties;
 import java.util.Set;
 
-import com.glencoesoftware.omero.ms.core.OmeroAmazonS3ClientFactory;
-import com.glencoesoftware.omero.ms.core.OmeroS3FileSystem;
-import com.glencoesoftware.omero.ms.core.OmeroS3ReadOnlySeekableByteChannel;
+import com.glencoesoftware.omero.zarr.OmeroAmazonS3ClientFactory;
+import com.glencoesoftware.omero.zarr.OmeroS3FileSystem;
+import com.glencoesoftware.omero.zarr.OmeroS3ReadOnlySeekableByteChannel;
 import com.google.common.base.Preconditions;
 import com.upplication.s3fs.attribute.S3BasicFileAttributes;
 

src/main/resources/blitz/blitz-ZarrPixelBuffer.xml

@@ -6,8 +6,10 @@
         Defines the beans for microservices.
   </description>
 
-  <bean name="/OMERO/Pixels" class="com.glencoesoftware.omero.ms.core.PixelsService"
-        parent="filesystem">
+  <alias name="${omero.pixeldata.pixels_service:ZarrPixelsService}" alias="/OMERO/Pixels"/>
+
+  <bean name="ZarrPixelsService" class="com.glencoesoftware.omero.zarr.ZarrPixelsService"
+        parent="filesystem" lazy-init="true">
     <!-- note constructor-args from parent bean -->
     <constructor-arg value="${omero.pixeldata.memoizer.dir}"/>
     <constructor-arg ref="MemoizerWait"/>

src/test/java/com/glencoesoftware/omero/ms/core/PixelsServiceTest.java

@@ -27,6 +27,8 @@
 import org.junit.Before;
 import org.junit.Test;
 
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+
 import omero.ApiUsageException;
 import omero.model.ExternalInfo;
 import omero.model.ExternalInfoI;
@@ -43,7 +45,7 @@
 
 public class PixelsServiceTest {
 
-  private PixelsService pixelsService;
+  private ZarrPixelsService pixelsService;
   private String uuid = UUID.randomUUID().toString();
   private String imageUri = "/data/ngff/image.zarr";
   private String labelUri = imageUri + "/0/labels/" + uuid;
@@ -58,7 +60,7 @@ public void setUp() throws IOException {
       pixelsDir.deleteOnExit();
       File memoDir = Files.createTempDirectory("memoizer").toFile();
       memoDir.deleteOnExit();
-      pixelsService = new PixelsService(
+      pixelsService = new ZarrPixelsService(
           pixelsDir.getAbsolutePath(), false, memoDir, 0L, null, null, null, null, 0, 0, 0);
       mask = new MaskI();
       image = new ImageI();

src/test/java/com/glencoesoftware/omero/ms/core/ZarrPixelBufferTest.java

@@ -45,6 +45,8 @@
 
 import picocli.CommandLine;
 import com.glencoesoftware.bioformats2raw.Converter;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+import com.glencoesoftware.omero.zarr.ZarrPixelBuffer;
 
 import loci.formats.FormatTools;
 import loci.formats.in.FakeReader;
@@ -68,10 +70,10 @@ public ZarrPixelBuffer createPixelBuffer(
                 pixels, path, maxPlaneWidth, maxPlaneHeight,
                 Caffeine.newBuilder()
                     .maximumSize(0)
-                    .buildAsync(PixelsService::getZarrMetadata),
+                    .buildAsync(ZarrPixelsService::getZarrMetadata),
                 Caffeine.newBuilder()
                     .maximumSize(0)
-                    .buildAsync(PixelsService::getZarrArray)
+                    .buildAsync(ZarrPixelsService::getZarrArray)
                 );
     }