Merge pull request #25 from sbesson/zarr_s3_support

Add support for OME-Zarr hosted on AWS S3
glencoesoftware · Jun 17, 2024 · 6e15a99 · 6e15a99
2 parents 3bb126a + cefbfcb
commit 6e15a99
Show file tree

Hide file tree

Showing 4 changed files with 13 additions and 18 deletions.
diff --git a/build.gradle b/build.gradle
@@ -37,7 +37,6 @@ configurations.all {
     exclude group: 'gnu.getopt'
     exclude group: 'net.sf.ehcache'
     exclude group: 'org.apache.commons'
-    exclude group: 'org.apache.httpcomponents'
     exclude group: 'org.apache.pdfbox'
     exclude group: 'org.apache.xmlgraphics'
     exclude group: 'org.ini4j'
@@ -56,7 +55,7 @@ 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:0.4.0'
+    implementation 'com.glencoesoftware.omero:omero-zarr-pixel-buffer:0.4.1'
     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'
@@ -97,3 +96,7 @@ distributions {
 applicationDefaultJvmArgs = [
     "-Dvertx.logger-delegate-factory-class-name=io.vertx.core.logging.SLF4JLogDelegateFactory"
 ]
+
+startScripts {
+  classpath = files('$APP_HOME/lib/*')
+}
diff --git a/src/dist/conf/config.yaml b/src/dist/conf/config.yaml
@@ -12,6 +12,7 @@ omero.server:
     omero.db.port: "5432"
     omero.db.user: "omero"
     omero.db.pass: "omero"
+    omero.pixeldata.pixels_service: "ZarrPixelsService"
     # OMERO_HOME/lib/scripts
     omero.script_repo_root: "/opt/omero/OMERO.current/lib/scripts"
 # Information about the session store.

diff --git a/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/TileRequestHandler.java b/src/main/java/com/glencoesoftware/omero/ms/pixelbuffer/TileRequestHandler.java
@@ -228,9 +228,11 @@ protected Pixels getPixels(omero.client client, Long imageId)
         try {
             return (Pixels) client.getSession().getQueryService().findByQuery(
                 "SELECT p FROM Pixels as p " +
-                "JOIN FETCH p.image " +
+                "JOIN FETCH p.image as i " +
+                "LEFT OUTER JOIN FETCH i.format " +
+                "LEFT OUTER JOIN FETCH i.details.externalInfo " +
                 "JOIN FETCH p.pixelsType " +
-                "WHERE p.image.id = :id",
+                "WHERE i.id = :id",
                 params, ctx
             );
         } finally {

diff --git a/src/main/resources/beanRefContext.xml b/src/main/resources/beanRefContext.xml
@@ -46,20 +46,9 @@
 
   <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="omero-ms-pixel-buffer-verticle"
         class="com.glencoesoftware.omero.ms.pixelbuffer.PixelBufferVerticle"