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qupath / qupath-extension-omero-web

QuPath extension to work with images through OMERO's web API
GNU General Public License v3.0
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NullPointerException when connecting to a private OMERO instance. #17

Open tinevez opened 2 years ago

tinevez commented 2 years ago

Hello,

We have an OMERO instance deployed on the campus that we can access via the webclient and Insight. We are trying to analyze images stored on OMERO with QuPath but fails only for our instance.

Using

When we try to add the OMERO server using Extensions > OMERO > Browser server... > New server, we enter the following: https://omero.**.**.fr

Then we receive the following NPE:

ERROR: Unable to connect to OMERO server: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null ERROR: QuPath exception: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null java.lang.NullPointerException: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null (Full stack below.)

I guess we did not configure our server properly, and are asking whether you would have insights as to what we should ook for / ask to IT people / OMERO people. We have no clue yet.

What is perturbing is that the extension works (beautifully) when we are trying to connect to the IDR. Best JY & Son

Full stack:

INFO: Refreshing extensions in /Users/tinevez/QuPath/v0.3/extensions
INFO: Added extension: /Users/tinevez/QuPath/v0.3/extensions/qupath-extension-omero-0.3.0.jar
INFO: Initializing type adapters
INFO: Bio-Formats version 6.7.0
INFO: Loaded extension Bio-Formats options (Bio-Formats 6.7.0) (11 ms)
INFO: Loaded extension ImageJ extension (39 ms)
INFO: Loaded extension OMERO extension (2 ms)
INFO: Loaded extension Processing extension (22 ms)
INFO: Loaded extension Rich script editor extension (50 ms)
INFO: Loaded extension SVG export extension (1 ms)
INFO: OpenSlide version 3.4.1
INFO: Starting QuPath with parameters: []
INFO: Project set to Project: TestOMEROQuPath-project
ERROR: Unable to connect to OMERO server: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null
ERROR: QuPath exception: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null
java.lang.NullPointerException: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null
    at qupath.lib.images.servers.omero.OmeroWebClient.loadURLs(OmeroWebClient.java:480)
    at qupath.lib.images.servers.omero.OmeroWebClient.<init>(OmeroWebClient.java:138)
    at qupath.lib.images.servers.omero.OmeroWebClient.create(OmeroWebClient.java:125)
    at qupath.lib.images.servers.omero.OmeroWebClients.createClientAndLogin(OmeroWebClients.java:150)
    at qupath.lib.images.servers.omero.OmeroExtension.lambda$createServerListMenu$1(OmeroExtension.java:159)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
    at com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(GlobalMenuAdapter.java:153)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
    at com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(GlassSystemMenu.java:234)
ERROR: QuPath exception: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null
java.lang.NullPointerException: Cannot invoke "java.util.Map.get(Object)" because "this.omeroURLs" is null
    at qupath.lib.images.servers.omero.OmeroWebClient.loadURLs(OmeroWebClient.java:480)
    at qupath.lib.images.servers.omero.OmeroWebClient.<init>(OmeroWebClient.java:138)
    at qupath.lib.images.servers.omero.OmeroWebClient.create(OmeroWebClient.java:125)
    at qupath.lib.images.servers.omero.OmeroWebClients.createClientAndLogin(OmeroWebClients.java:150)
    at qupath.lib.images.servers.omero.OmeroExtension.lambda$createServerListMenu$1(OmeroExtension.java:159)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
    at com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(GlobalMenuAdapter.java:153)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.control.MenuItem.fire(MenuItem.java:459)
    at com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(GlassSystemMenu.java:234)