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BIOP / qupath-extension-biop-omero

QuPath extension to work with images through OMERO's Java API (raw)
GNU General Public License v3.0
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not available in Extensions menu (Renku-Linux) #6

Closed romainGuiet closed 2 years ago

romainGuiet commented 2 years ago

On Renku-Linux : 

Version: 0.3.2
Build time: 2022-01-17, 08:49
Latest commit tag: '71884c6'

Java version:       16.0.2
Java vendor:        Eclipse Foundation  -  https://adoptium.net/
Java home:          /opt/QuPath/lib/runtime

Operating system:       Linux  -  3.10.0-1160.42.2.el7.x86_64
Architecture:           amd64

Number of available processors:     32

Memory already used by JVM:         123 MB
Total memory currently available:       224 MB
Max memory JVM may try to use:      1908 MB
--- WARNING: Max memory is quite low (< 4GB)  - may not be enough to run full whole slide analysis.

Library path:
      /opt/QuPath/lib/app

Class path:
      /opt/QuPath/lib/app/qupath-app-0.3.2.jar
      /opt/QuPath/lib/app/JWlz-1.4.0.jar
      /opt/QuPath/lib/app/asm-5.0.4.jar
      /opt/QuPath/lib/app/c3p0-0.9.5.3.jar
      /opt/QuPath/lib/app/cdm-4.6.13.jar
      /opt/QuPath/lib/app/checker-qual-3.8.0.jar
      /opt/QuPath/lib/app/commons-io-1.4.jar
      /opt/QuPath/lib/app/commons-lang-2.4.jar
      /opt/QuPath/lib/app/commons-lang3-3.11.jar
      /opt/QuPath/lib/app/commons-math3-3.6.1.jar
      /opt/QuPath/lib/app/commons-text-1.9.jar
      /opt/QuPath/lib/app/controlsfx-11.1.1.jar
      /opt/QuPath/lib/app/error_prone_annotations-2.5.1.jar
      /opt/QuPath/lib/app/failureaccess-1.0.1.jar
      /opt/QuPath/lib/app/flowless-0.6.7.jar
      /opt/QuPath/lib/app/formats-api-6.7.0.jar
      /opt/QuPath/lib/app/formats-bsd-6.7.0.jar
      /opt/QuPath/lib/app/formats-gpl-6.7.0.jar
      /opt/QuPath/lib/app/groovy-3.0.9.jar
      /opt/QuPath/lib/app/groovy-jsr223-3.0.9.jar
      /opt/QuPath/lib/app/groovy-xml-3.0.9.jar
      /opt/QuPath/lib/app/gson-2.8.9.jar
      /opt/QuPath/lib/app/guava-30.1.1-jre.jar
      /opt/QuPath/lib/app/httpclient-4.5.1.jar
      /opt/QuPath/lib/app/httpmime-4.5.1.jar
      /opt/QuPath/lib/app/httpservices-4.6.13.jar
      /opt/QuPath/lib/app/ij-1.53i.jar
      /opt/QuPath/lib/app/j2objc-annotations-1.3.jar
      /opt/QuPath/lib/app/jackson-annotations-2.9.8.jar
      /opt/QuPath/lib/app/jackson-core-2.9.8.jar
      /opt/QuPath/lib/app/jackson-databind-2.9.8.jar
      /opt/QuPath/lib/app/javacpp-1.5.6-linux-x86_64.jar
      /opt/QuPath/lib/app/javacpp-1.5.6.jar
      /opt/QuPath/lib/app/javacpp-platform-1.5.6.jar
      /opt/QuPath/lib/app/javafx-base-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-base-17.0.1.jar
      /opt/QuPath/lib/app/javafx-controls-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-controls-17.0.1.jar
      /opt/QuPath/lib/app/javafx-graphics-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-graphics-17.0.1.jar
      /opt/QuPath/lib/app/javafx-media-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-media-17.0.1.jar
      /opt/QuPath/lib/app/javafx-swing-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-swing-17.0.1.jar
      /opt/QuPath/lib/app/javafx-web-17.0.1-linux.jar
      /opt/QuPath/lib/app/javafx-web-17.0.1.jar
      /opt/QuPath/lib/app/jfxtras-common-11-r2.jar
      /opt/QuPath/lib/app/jfxtras-menu-11-r2.jar
      /opt/QuPath/lib/app/jgoodies-common-1.7.0.jar
      /opt/QuPath/lib/app/jgoodies-forms-1.7.2.jar
      /opt/QuPath/lib/app/jhdf5-14.12.6.jar
      /opt/QuPath/lib/app/joda-time-2.8.1.jar
      /opt/QuPath/lib/app/json-20090211.jar
      /opt/QuPath/lib/app/jts-core-1.18.2.jar
      /opt/QuPath/lib/app/jxrlib-all-0.2.4.jar
      /opt/QuPath/lib/app/kryo-4.0.2.jar
      /opt/QuPath/lib/app/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
      /opt/QuPath/lib/app/logback-classic-1.2.9.jar
      /opt/QuPath/lib/app/logback-core-1.2.9.jar
      /opt/QuPath/lib/app/mchange-commons-java-0.2.15.jar
      /opt/QuPath/lib/app/metadata-extractor-2.11.0.jar
      /opt/QuPath/lib/app/metakit-5.3.3.jar
      /opt/QuPath/lib/app/minlog-1.3.0.jar
      /opt/QuPath/lib/app/native-lib-loader-2.1.4.jar
      /opt/QuPath/lib/app/objenesis-2.5.1.jar
      /opt/QuPath/lib/app/ome-codecs-0.3.1.jar
      /opt/QuPath/lib/app/ome-common-6.0.7.jar
      /opt/QuPath/lib/app/ome-jai-0.1.0.jar
      /opt/QuPath/lib/app/ome-mdbtools-5.3.2.jar
      /opt/QuPath/lib/app/ome-poi-5.3.4.jar
      /opt/QuPath/lib/app/ome-xml-6.2.3.jar
      /opt/QuPath/lib/app/openblas-0.3.17-1.5.6-linux-x86_64.jar
      /opt/QuPath/lib/app/openblas-0.3.17-1.5.6.jar
      /opt/QuPath/lib/app/openblas-platform-0.3.17-1.5.6.jar
      /opt/QuPath/lib/app/opencv-4.5.3-1.5.6-linux-x86_64.jar
      /opt/QuPath/lib/app/opencv-4.5.3-1.5.6.jar
      /opt/QuPath/lib/app/opencv-platform-4.5.3-1.5.6.jar
      /opt/QuPath/lib/app/openslide-3.4.1_2-natives-linux.jar
      /opt/QuPath/lib/app/openslide-3.4.1_2.jar
      /opt/QuPath/lib/app/org.jfree.svg-5.0.jar
      /opt/QuPath/lib/app/perf4j-0.9.16.jar
      /opt/QuPath/lib/app/picocli-4.6.2.jar
      /opt/QuPath/lib/app/qupath-core-0.3.2.jar
      /opt/QuPath/lib/app/qupath-core-processing-0.3.2.jar
      /opt/QuPath/lib/app/qupath-extension-bioformats-0.3.2.jar
      /opt/QuPath/lib/app/qupath-extension-openslide-0.3.2.jar
      /opt/QuPath/lib/app/qupath-extension-processing-0.3.2.jar
      /opt/QuPath/lib/app/qupath-extension-script-editor-0.3.2.jar
      /opt/QuPath/lib/app/qupath-extension-svg-0.3.2.jar
      /opt/QuPath/lib/app/qupath-gui-fx-0.3.2.jar
      /opt/QuPath/lib/app/reactfx-2.0-M5.jar
      /opt/QuPath/lib/app/reflectasm-1.11.3.jar
      /opt/QuPath/lib/app/richtextfx-0.10.7.jar
      /opt/QuPath/lib/app/slf4j-api-1.7.32.jar
      /opt/QuPath/lib/app/specification-6.2.3.jar
      /opt/QuPath/lib/app/sqlite-jdbc-3.28.0.jar
      /opt/QuPath/lib/app/turbojpeg-6.7.0.jar
      /opt/QuPath/lib/app/undofx-2.1.1.jar
      /opt/QuPath/lib/app/wellbehavedfx-0.3.3.jar
      /opt/QuPath/lib/app/xercesImpl-2.8.1.jar
      /opt/QuPath/lib/app/xml-apis-1.3.03.jar
      /opt/QuPath/lib/app/xmpcore-5.1.3.jar

The Extensions > OMERO-Raw doesn't appear and I get the error below when starting QuPath : 

INFO: Refreshing extensions in /home/jovyan/Desktop/QuPath_Common_Data/extensions
INFO: Added extension: /home/jovyan/Desktop/QuPath_Common_Data/extensions/qupath-extension-biop-omero-0.1.5.jar
INFO: Initializing type adapters
INFO: Bio-Formats version 6.7.0
INFO: Loaded extension Bio-Formats options (Bio-Formats 6.7.0) (15 ms)
INFO: Loaded extension ImageJ extension (53 ms)
ERROR: Error loading extension qupath.ext.biop.servers.omero.raw.OmeroRawExtension@611115aa: omero/gateway/exception/DSOutOfServiceException
java.lang.NoClassDefFoundError: omero/gateway/exception/DSOutOfServiceException
    at qupath.ext.biop.servers.omero.raw.OmeroRawExtension.installExtension(OmeroRawExtension.java:76)
    at qupath.lib.gui.QuPathGUI.refreshExtensions(QuPathGUI.java:1698)
    at qupath.lib.gui.QuPathGUI.<init>(QuPathGUI.java:1110)
    at qupath.lib.gui.QuPathApp.start(QuPathApp.java:61)
    at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
    at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
    at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
    at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
    at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
    at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:290)
    at java.base/java.lang.Thread.run(Unknown Source)
  Caused by omero.gateway.exception.DSOutOfServiceException        at java.base/java.net.URLClassLoader.findClass(Unknown Source)
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source)
        at qupath.ext.biop.servers.omero.raw.OmeroRawExtension.installExtension(OmeroRawExtension.java:76)
        at qupath.lib.gui.QuPathGUI.refreshExtensions(QuPathGUI.java:1698)
        at qupath.lib.gui.QuPathGUI.<init>(QuPathGUI.java:1110)
        at qupath.lib.gui.QuPathApp.start(QuPathApp.java:61)
        at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:847)
        at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:484)
        at com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
        at java.base/java.security.AccessController.doPrivileged(Unknown Source)
        at com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
        at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
        at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
        at com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(GtkApplication.java:290)
        at java.base/java.lang.Thread.run(Unknown Source)
WARN: 'OMERO BIOP extension' was written for QuPath 0.1.5 but current version is 0.3.2
ERROR: It is recommended that you delete file:/home/jovyan/Desktop/QuPath_Common_Data/extensions/qupath-extension-biop-omero-0.1.5.jar and restart QuPath
INFO: Loaded extension Processing extension (27 ms)
INFO: Loaded extension Rich script editor extension (67 ms)
INFO: Loaded extension SVG export extension (1 ms)
INFO: OpenSlide version 3.4.1
INFO: Starting QuPath with parameters: []
Rdornier commented 2 years ago

Hello,

It looks for the gateway but cannot find the class. You need to add the OMERO library. You can download OMERO-Fiji plugin omero-ij_5.x.x-all.jar and add it to the extension folder (next to the qupath-extension-biop-omero-x.x.x.jar).

You have also instructions in the readme.

romainGuiet commented 2 years ago

Works !