Merge pull request #23 from sbesson/omero_zarr_pixel-buffer_0.3.0

Expose omero-zarr-pixel-buffer in pixel-buffer micro-service
glencoesoftware · May 17, 2024 · 3bb126a · 3bb126a
2 parents bc9288a + 0c27de2
commit 3bb126a
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Showing 6 changed files with 30 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ Requirements
 * OMERO 5.6.x+
 * OMERO.web 5.6.x+
 * Redis backed sessions
-* Java 8+
+* Java 11+
 
 Workflow
 ========

diff --git a/build.gradle b/build.gradle
@@ -4,12 +4,12 @@ plugins {
 }
 
 group = 'com.glencoesoftware.omero'
-version = '0.6.5-SNAPSHOT'
+version = '0.7.0-SNAPSHOT'
 
 mainClassName = 'io.vertx.core.Launcher'
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+sourceCompatibility = 1.11
+targetCompatibility = 1.11
 
 repositories {
     mavenCentral()
@@ -56,11 +56,12 @@ 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-ms-core:0.7.0'
+    implementation 'com.glencoesoftware.omero:omero-zarr-pixel-buffer:0.4.0'
+    implementation 'com.glencoesoftware.omero:omero-ms-core:0.9.0'
     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'
-    implementation 'org.openmicroscopy:omero-blitz:5.7.2'
+    implementation 'org.openmicroscopy:omero-blitz:5.7.3'
     implementation 'io.prometheus.jmx:collector:0.12.0'
     implementation 'io.prometheus:simpleclient_hotspot:0.8.0'
     implementation 'com.zeroc:icegrid:3.6.4'

diff --git a/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/Main.java b/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/Main.java
@@ -14,6 +14,7 @@ public static void main(String[] args) {
         ApplicationContext context = new ClassPathXmlApplicationContext(
                 "classpath:ome/config.xml",
                 "classpath:ome/services/datalayer.xml",
+                "classpath*:blitz/*PixelBuffer.xml",
                 "classpath*:beanRefContext.xml");
         PixelsService bean = (PixelsService) context.getBean("/OMERO/Pixels");
         System.err.println("Bean: " + bean);

diff --git a/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/PixelBufferMicroserviceVerticle.java b/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/PixelBufferMicroserviceVerticle.java
@@ -157,8 +157,8 @@ public void deploy(JsonObject config, Promise<Void> prom) {
         context = new ClassPathXmlApplicationContext(
                 "classpath:ome/config.xml",
                 "classpath:ome/services/datalayer.xml",
-                "classpath*:beanRefContext.xml",
-                "classpath*:service-ms.core.PixelsService.xml");
+                "classpath*:blitz/*PixelBuffer.xml",
+                "classpath*:beanRefContext.xml");
 
         JsonObject httpTracingConfig =
                 config.getJsonObject("http-tracing", new JsonObject());

diff --git a/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/PixelBufferVerticle.java b/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/PixelBufferVerticle.java
@@ -26,7 +26,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.glencoesoftware.omero.ms.core.OmeroMsAbstractVerticle;
 import com.glencoesoftware.omero.ms.core.OmeroRequest;
-import com.glencoesoftware.omero.ms.core.PixelsService;
+import com.glencoesoftware.omero.zarr.ZarrPixelsService;
 
 import Glacier2.CannotCreateSessionException;
 import Glacier2.PermissionDeniedException;
@@ -53,7 +53,7 @@ public class PixelBufferVerticle extends OmeroMsAbstractVerticle {
             "omero.pixel_buffer.get_tile";
 
     /** OMERO server pixels service. */
-    private final PixelsService pixelsService;
+    private final ZarrPixelsService pixelsService;
 
     /** OMERO server host */
     private String host;
@@ -66,7 +66,7 @@ public class PixelBufferVerticle extends OmeroMsAbstractVerticle {
      * @param host OMERO server host.
      * @param port OMERO server port.
      */
-    public PixelBufferVerticle(PixelsService pixelsService) {
+    public PixelBufferVerticle(ZarrPixelsService pixelsService) {
         this.pixelsService = pixelsService;
     }
 

diff --git a/src/main/resources/beanRefContext.xml b/src/main/resources/beanRefContext.xml
@@ -8,6 +8,7 @@
 
   <bean name="filesystem"  abstract="true">
     <constructor-arg index="0" value="${omero.data.dir}"/>
+    <constructor-arg index="1" type="boolean" value="true"/>
   </bean>
 
   <bean id="omeroFilePathResolver" class="ome.services.OmeroFilePathResolver">
@@ -43,8 +44,23 @@
     <property name="graphiteAddress" value="${omero.metrics.graphite}"/>
   </bean>
 
-  <bean id="nullMetrics" class="ome.system.metrics.NullMetrics"/>
+  <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="omero-ms-pixel-buffer-verticle"
         class="com.glencoesoftware.omero.ms.pixelbuffer.PixelBufferVerticle"
         scope="prototype">