Merge pull request #142 from sbesson/pixelsservice_runtime_improvements

Allow the PixelsService to be runtime configured

build.gradle

@@ -62,8 +62,8 @@ dependencies {
     implementation 'io.zipkin.reporter2:zipkin-sender-okhttp3:2.10.0'
     implementation 'ch.qos.logback:logback-classic:1.3.14'
     implementation 'org.slf4j:log4j-over-slf4j:1.7.32'
-    implementation 'com.glencoesoftware.omero:omero-zarr-pixel-buffer:0.3.0'
-    implementation 'com.glencoesoftware.omero:omero-ms-core:0.8.0'
+    implementation 'com.glencoesoftware.omero:omero-zarr-pixel-buffer:0.4.0-SNAPSHOT'
+    implementation 'com.glencoesoftware.omero:omero-ms-core:0.9.0-SNAPSHOT'
     implementation 'io.vertx:vertx-web:3.8.1'
     implementation 'io.vertx:vertx-config:3.8.1'
     implementation 'io.vertx:vertx-config-yaml:3.8.1'

src/dist/conf/config.yaml

@@ -31,6 +31,7 @@ omero.server:
     # The following should be set to match your OMERO.web settings
     # See https://docs.openmicroscopy.org/omero/5.6.3/sysadmins/config.html#omero-client-viewer-interpolate-pixels
     # and https://docs.openmicroscopy.org/omero/5.6.3/sysadmins/config.html#omero-client-viewer-initial-zoom-level
+    omero.pixeldata.pixels_service: "ZarrPixelsService"
     omero.pixeldata.zarr_cache_size: "500"
     omero.client.viewer.initial_zoom_level: "0"
     omero.client.viewer.interpolate_pixels: "true"

src/main/java/com/glencoesoftware/omero/ms/image/region/HistogramRequestHandler.java

@@ -18,6 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -59,15 +61,15 @@ public class HistogramRequestHandler {
     HistogramCtx histogramCtx;
 
     /** OMERO server pixels service. */
-    private PixelsService pixelsService;
+    private ZarrPixelsService pixelsService;
 
     /**
      * Constructor. Populates histogramCtx and pixelsService
      * @param histogramCtx
      * @param pixelsService
      */
     public HistogramRequestHandler(HistogramCtx histogramCtx,
-            PixelsService pixelsService) {
+            ZarrPixelsService pixelsService) {
         this.histogramCtx = histogramCtx;
         this.pixelsService = pixelsService;
     }

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageDataRequestHandler.java

@@ -18,6 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -76,7 +78,7 @@ public class ImageDataRequestHandler {
     private ImageDataCtx imageDataCtx;
 
     /** OMERO server pixels service. */
-    private PixelsService pixelsService;
+    private ZarrPixelsService pixelsService;
 
     /** Initial Zoom level from server settings **/
     private int initZoom;
@@ -92,7 +94,7 @@ public class ImageDataRequestHandler {
      * @param interpolate Interpolation server setting
      */
     public ImageDataRequestHandler(ImageDataCtx imageDataCtx,
-            PixelsService pixelsService,
+            ZarrPixelsService pixelsService,
             int initZoom, boolean interpolate) {
         this.imageDataCtx = imageDataCtx;
         this.pixelsService = pixelsService;

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionMicroserviceVerticle.java

@@ -171,6 +171,7 @@ public void deploy(JsonObject config, Promise<Void> prom) {
         context = new ClassPathXmlApplicationContext(
                 "classpath:ome/config.xml",
                 "classpath:ome/services/datalayer.xml",
+                "classpath*:blitz/*PixelBuffer.xml",
                 "classpath*:beanRefContext.xml");
         preferences =
                 (PreferenceContext) this.context.getBean("preferenceContext");

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionRequestHandler.java

@@ -18,6 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+
 import java.awt.Dimension;
 import java.awt.image.BufferedImage;
 import java.io.ByteArrayOutputStream;
@@ -90,7 +92,7 @@ public class ImageRegionRequestHandler {
     protected final List<RenderingModel> renderingModels;
 
     /** OMERO server pixels service. */
-    protected final PixelsService pixelsService;
+    protected final ZarrPixelsService pixelsService;
 
     /** Reference to the projection service. */
     private final ProjectionService projectionService;
@@ -112,7 +114,7 @@ public ImageRegionRequestHandler(
             LutProvider lutProvider,
             LocalCompress compressionSrv,
             int maxTileLength,
-            PixelsService pixelsService) {
+            ZarrPixelsService pixelsService) {
         this.compressionSrv = compressionSrv;
         this.lutProvider = lutProvider;
         this.families = families;

src/main/java/com/glencoesoftware/omero/ms/image/region/ImageRegionVerticle.java

@@ -31,6 +31,7 @@
 import com.glencoesoftware.omero.ms.core.OmeroMsAbstractVerticle;
 import com.glencoesoftware.omero.ms.core.OmeroRequest;
 import com.glencoesoftware.omero.ms.core.RedisCacheVerticle;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
 
 import Glacier2.CannotCreateSessionException;
 import Glacier2.PermissionDeniedException;
@@ -92,7 +93,7 @@ public class ImageRegionVerticle extends OmeroMsAbstractVerticle {
     /** Configured maximum size size in either dimension */
     private final int maxTileLength;
 
-    private final PixelsService pixelsService;
+    private final ZarrPixelsService pixelsService;
 
     /** Scaling service for thumbnails */
     private final IScale iScale;
@@ -104,7 +105,7 @@ public ImageRegionVerticle(
             LocalCompress compressionService,
             LutProvider lutProvider,
             int maxTileLength,
-            PixelsService pixelsService,
+            ZarrPixelsService pixelsService,
             IScale iScale)
     {
         this.compressionService = compressionService;

src/main/java/com/glencoesoftware/omero/ms/image/region/ShapeMaskRequestHandler.java

@@ -18,7 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
-import com.glencoesoftware.omero.ms.core.ZarrPixelBuffer;
+import com.glencoesoftware.omero.zarr.ZarrPixelBuffer;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
 
 import java.awt.Point;
 import java.awt.image.BufferedImage;
@@ -69,15 +70,15 @@ public class ShapeMaskRequestHandler {
     private final ShapeMaskCtx shapeMaskCtx;
 
     /** Configured Pixels service */
-    private final PixelsService pixelsService;
+    private final ZarrPixelsService pixelsService;
 
     /**
      * Default constructor.
      * @param shapeMaskCtx {@link ShapeMaskCtx} object
      * @param pixelsService configured pixels service
      */
     public ShapeMaskRequestHandler(
-            ShapeMaskCtx shapeMaskCtx, PixelsService pixelsService) {
+            ShapeMaskCtx shapeMaskCtx, ZarrPixelsService pixelsService) {
         log.info("Setting up handler");
         this.shapeMaskCtx = shapeMaskCtx;
         this.pixelsService = pixelsService;

src/main/java/com/glencoesoftware/omero/ms/image/region/ShapeMaskVerticle.java

@@ -24,6 +24,7 @@
 import com.glencoesoftware.omero.ms.core.OmeroMsAbstractVerticle;
 import com.glencoesoftware.omero.ms.core.OmeroRequest;
 import com.glencoesoftware.omero.ms.core.RedisCacheVerticle;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
 
 import Glacier2.CannotCreateSessionException;
 import Glacier2.PermissionDeniedException;
@@ -55,12 +56,12 @@ public class ShapeMaskVerticle extends OmeroMsAbstractVerticle {
     private int port;
 
     /** Configured Pixels service */
-    private final PixelsService pixelsService;
+    private final ZarrPixelsService pixelsService;
 
     /**
      * Default constructor.
      */
-    public ShapeMaskVerticle(PixelsService pixelsService)
+    public ShapeMaskVerticle(ZarrPixelsService pixelsService)
     {
         this.pixelsService = pixelsService;
     }

src/main/java/com/glencoesoftware/omero/ms/image/region/ThumbnailsRequestHandler.java

@@ -18,6 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
+
 import java.awt.image.BufferedImage;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -74,7 +76,7 @@ public ThumbnailsRequestHandler(
             LutProvider lutProvider,
             LocalCompress compressionSrv,
             int maxTileLength,
-            PixelsService pixelsService,
+            ZarrPixelsService pixelsService,
             IScale iScale) {
         super(thumbnailCtx,
                 families,

src/main/resources/beanRefContext.xml

@@ -52,21 +52,10 @@
   </bean>
 
   <bean id="metrics" class="ome.system.metrics.NullMetrics"/>
-
-  <bean name="/OMERO/Pixels" class="com.glencoesoftware.omero.ms.image.region.PixelsService"
-        parent="filesystem">
-    <!-- index=0 "path" comes from parent -->
-    <constructor-arg index="2" value="${omero.pixeldata.memoizer.dir}"/>
-    <constructor-arg index="3" ref="MemoizerWait"/>
-    <constructor-arg index="4" ref="omeroFilePathResolver"/>
-    <constructor-arg index="5" ref="backOff"/>
-    <constructor-arg index="6" ref="tileSizes"/>
-    <constructor-arg index="7" ><null /></constructor-arg>
-    <constructor-arg index="8" value="${omero.pixeldata.zarr_cache_size:500}" />
-    <constructor-arg index="9" value="${omero.pixeldata.max_plane_width:3192}" />
-    <constructor-arg index="10" value="${omero.pixeldata.max_plane_height:3192}" />
-    <property name="metrics" ref="metrics"/>
-  </bean>
+
+  <bean id="internal-ome.api.IQuery" class="com.glencoesoftware.omero.ms.core.NoopQueryImpl"/>
+
+  <alias name="${omero.pixeldata.pixels_service:ZarrPixelsService}" alias="/OMERO/Pixels"/>
 
   <bean id="iscale" class="ome.logic.JavaImageScalingService"/>
 

src/test/java/com/glencoesoftware/omero/ms/image/region/ImageDataRequestHandlerTest.java

@@ -18,7 +18,8 @@
 
 package com.glencoesoftware.omero.ms.image.region;
 
-import com.glencoesoftware.omero.ms.core.ZarrPixelBuffer;
+import com.glencoesoftware.omero.zarr.ZarrPixelBuffer;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
 
 import java.io.File;
 import java.io.IOException;
@@ -409,10 +410,10 @@ public void createPixelBuffer() throws IOException, ApiUsageException {
                 output.resolve("0"), 1024, 1024,
                 Caffeine.newBuilder()
                     .maximumSize(0)
-                    .buildAsync(PixelsService::getZarrMetadata),
+                    .buildAsync(ZarrPixelsService::getZarrMetadata),
                 Caffeine.newBuilder()
                     .maximumSize(0)
-                    .buildAsync(PixelsService::getZarrArray));
+                    .buildAsync(ZarrPixelsService::getZarrArray));
     }
 
     @Before