Modify extension to request raw tiles when possible

.github/workflows/build_jar.yml

@@ -9,17 +9,17 @@
    build:
      runs-on: ubuntu-latest
      steps:
-     - uses: actions/checkout@v2
-     - name: Set up JDK 11
-       uses: actions/setup-java@v2
+     - uses: actions/checkout@v4
+     - name: Set up JDK 17
+       uses: actions/setup-java@v4
        with:
-         java-version: '11'
+         java-version: '17'
          distribution: 'adopt-hotspot'
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
      - name: Build with Gradle
-       run: ./gradlew build -P toolchain=11
-     - uses: actions/upload-artifact@v2
+       run: ./gradlew build -P toolchain=17
+     - uses: actions/upload-artifact@v4
        with:
          name: libs
          path: build/libs

.github/workflows/gradle.yml

@@ -1,21 +1,29 @@
 # This workflow will build a Java project with Gradle
  # For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-gradle
 
- name: Java CI with Gradle
+name: Java CI with Gradle
 
- on: [pull_request]
+on:
+  push:
+  pull_request:
 
- jobs:
-   build:
-     runs-on: ubuntu-latest
-     steps:
-     - uses: actions/checkout@v2
-     - name: Set up JDK 11
-       uses: actions/setup-java@v2
-       with:
-         java-version: '11'
-         distribution: 'adopt-hotspot'
-     - name: Grant execute permission for gradlew
-       run: chmod +x gradlew
-     - name: Build with Gradle
-       run: ./gradlew build -P toolchain=11
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          java-version: '17'
+          distribution: 'adopt-hotspot'
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+      - name: Build with Gradle
+        run: ./gradlew build -P toolchain=17
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: qupath-extension-omero-gs
+          path: build/libs/*.jar
+          retention-days: 30

README.md

@@ -1,14 +1,13 @@
-[![Extension docs](https://img.shields.io/badge/docs-qupath_omero-red)](https://qupath.readthedocs.io/en/stable/docs/advanced/omero.html)
-[![Forum](https://img.shields.io/badge/forum-image.sc-green)](https://forum.image.sc/tag/qupath)
-[![Downloads (latest release)](https://img.shields.io/github/downloads-pre/qupath/qupath-extension-omero/latest/total)](https://github.com/qupath/qupath-extension-omero/releases/latest)
-[![Downloads (all releases)](https://img.shields.io/github/downloads/qupath/qupath-extension-omero/total)](https://github.com/qupath/qupath-extension-omero/releases)
+# QuPath OMERO extension with raw tiles support
 
-# QuPath OMERO extension
-
-Welcome to the OMERO extension for [QuPath](http://qupath.github.io)!
+Welcome to the Glencoe Software's version of the OMERO extension for [QuPath](http://qupath.github.io)!
 
 This adds support for accessing images hosted on an [OMERO](https://www.openmicroscopy.org/omero/) 
-server through OMERO's web API.
+server.  If microservices are available on the OMERO server, then they will be used to retrieve
+image data; all data types are supported in this case, and uncompressed image data is provided to QuPath.
+
+If microservices are not available, then the OMERO web API is used. In this case, only uint8 images
+with 3 or fewer channels are supported.
 
 > **Important!**
 > 
@@ -29,7 +28,7 @@ The main documentation for the extension is at https://qupath.readthedocs.io/en/
 
 ## Installing
 
-To install the OMERO extension, download the latest `qupath-extension-omero-[version].jar` file from [releases](https://github.com/qupath/qupath-extension-omero/releases) and drag it onto the main QuPath window.
+To install the OMERO extension, download the latest `qupath-extension-omero-[version].jar` file from [releases](https://github.com/glencoesoftware/qupath-extension-omero/releases) and drag it onto the main QuPath window.
 
 If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory.
 The extension will then be copied to a location inside that directory.

build.gradle

@@ -8,35 +8,36 @@ plugins {
 }
 
 ext.moduleName = 'qupath.extension.omero'
-ext.qupathVersion = gradle.ext.qupathVersion
 ext.qupathJavaVersion = 17
-
-base {
-    description = "QuPath extension to support image reading using OMERO's web API."
-    version = "0.4.0"
-    group = "io.github.qupath"
-}
+archivesBaseName = 'qupath-extension-omero'
+description = "QuPath extension to support image reading using OMERO's web API."
+version = "0.4.1-gs-SNAPSHOT"
 
 repositories {
-
+  mavenLocal()
   mavenCentral()
-  
+
   maven {
-    url "https://maven.scijava.org/content/repositories/releases"
+    url 'https://artifacts.glencoesoftware.com/artifactory/scijava-thirdparty'
   }
-  
+
   maven {
-    url "https://maven.scijava.org/content/repositories/snapshots"
+    url 'https://artifacts.glencoesoftware.com/artifactory/ome.releases'
   }
-
+
+  maven {
+    url "https://maven.scijava.org/content/repositories/releases"
+  }
+
 }
 
 dependencies {
-    implementation libs.commons.text
-    shadow "io.github.qupath:qupath-gui-fx:${qupathVersion}"
-    shadow libs.qupath.fxtras
-
-    shadow libs.slf4j
+  implementation "org.apache.commons:commons-text:1.9"
+
+  shadow "io.github.qupath:qupath-gui-fx:0.5.1"    
+  shadow "io.github.qupath:qupath-fxtras:0.1.4"
+  shadow "ome:formats-bsd:7.0.1"
+  shadow "org.slf4j:slf4j-api:1.7.30"
 }
 
 jar {
@@ -88,3 +89,15 @@ tasks.withType(org.gradle.jvm.tasks.Jar) {
 tasks.named('test') {
     useJUnitPlatform()
 }
+
+javafx {
+	version = "17.0.9"
+	modules = ["javafx.base",
+	           "javafx.controls",
+	           "javafx.graphics",
+	           "javafx.media",
+	           "javafx.fxml",
+	           "javafx.web",
+	           "javafx.swing"]
+	configuration = 'api'
+}

src/main/java/qupath/lib/images/servers/omero/OmeroExtension.java

@@ -26,12 +26,19 @@
 import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.google.gson.Gson;
+import com.google.gson.JsonSyntaxException;
+import com.google.gson.reflect.TypeToken;
+
+import javafx.beans.property.StringProperty;
 import javafx.event.Event;
 import javafx.event.EventHandler;
 import javafx.scene.control.Label;
@@ -46,6 +53,7 @@
 import qupath.lib.gui.actions.ActionTools;
 import qupath.lib.gui.extensions.GitHubProject;
 import qupath.lib.gui.extensions.QuPathExtension;
+import qupath.lib.gui.prefs.PathPrefs;
 import qupath.lib.gui.tools.MenuTools;
 
 /**
@@ -102,16 +110,23 @@ public String getDescription() {
 
 	private static Menu createServerListMenu(QuPathGUI qupath, Menu browseServerMenu) {
 		EventHandler<Event> validationHandler = e -> {
+      StringProperty usedServerProp = PathPrefs.createPersistentPreference("omero_ext.server_list", "");
+
+      List<String> usedServers = getServerList(usedServerProp);
+
 			browseServerMenu.getItems().clear();
 
 			// Get all active servers
 			var activeServers = OmeroWebClients.getAllClients();
 
 			// Populate the menu with each unique active servers
+      ArrayList<String> activeURIs = new ArrayList<String>();
 			for (var client: activeServers) {
 				if (client == null)
 					continue;
+        // 3 dots are appended to distinguish active connections
 				MenuItem item = new MenuItem(client.getServerURI() + "...");
+        activeURIs.add(client.getServerURI().toString());
 				item.setOnAction(e2 -> {
 					var browser = browsers.get(client);
 					if (browser == null || browser.getStage() == null) {
@@ -123,6 +138,23 @@ private static Menu createServerListMenu(QuPathGUI qupath, Menu browseServerMenu
 				});
 				browseServerMenu.getItems().add(item);
 			}
+
+      // add servers that have been connected to previously,
+      // but which are not currently connected
+      if (usedServers != null) {
+        for (String server : usedServers) {
+          final String usedServer = server.endsWith("/") ? server.substring(0, server.length() - 1) : server;
+          if (!usedServer.isEmpty() && !activeURIs.contains(usedServer)) {
+            // no suffix appended to the server name here
+            // distinguishes from active connections that have 3 dots appended
+            MenuItem item = new MenuItem(usedServer);
+            item.setOnAction(e2 -> {
+              handleLogin(qupath, usedServer);
+            });
+            browseServerMenu.getItems().add(item);
+          }
+        }
+      }
 
 			// Create 'New server...' MenuItem
 			MenuItem customServerItem = new MenuItem("New server...");
@@ -140,50 +172,73 @@ private static Menu createServerListMenu(QuPathGUI qupath, Menu browseServerMenu
 		        var path = tf.getText();
 				if (path == null || path.isEmpty())
 					return;
-				try {
-					if (!path.startsWith("http:") && !path.startsWith("https:"))
-						throw new IOException("The input URL must contain a scheme (e.g. \"https://\")!");
-
-					// Make the path a URI
-					URI uri = new URI(path);
-
-					// Clean the URI (in case it's a full path)
-					URI uriServer = OmeroTools.getServerURI(uri);
-
-					if (uriServer == null)
-						throw new MalformedURLException("Could not parse server from " + uri.toString());
-
-					// Check if client exist and if browser is already opened
-					var client = OmeroWebClients.getClientFromServerURI(uriServer);
-					if (client == null)
-						client = OmeroWebClients.createClientAndLogin(uriServer);
-
-					if (client == null)
-						throw new IOException("Could not parse server from " + uri.toString());
-
-					var browser = browsers.get(client);
-					if (browser == null || browser.getStage() == null) {
-						// Create new browser
-						browser = new OmeroWebImageServerBrowserCommand(qupath, client);
-						browsers.put(client, browser);
-						browser.run();
-					} else	// Request focus for already-existing browser
-						browser.getStage().requestFocus();		
-
-				} catch (FileNotFoundException ex) {
-					Dialogs.showErrorMessage("OMERO web server", String.format("An error occured when trying to reach %s: %s\"", path, ex.getLocalizedMessage()));
-				} catch (IOException | URISyntaxException ex) {
-					Dialogs.showErrorMessage("OMERO web server", ex.getLocalizedMessage());
-					return;
-				}
+
+        handleLogin(qupath, path);
+
+        List<String> serverList = getServerList(usedServerProp);
+        if (serverList != null && !serverList.contains(path)) {
+          serverList.add(path);
+          usedServerProp.setValue((new Gson()).toJson(serverList));
+        }
 			});
 			MenuTools.addMenuItems(browseServerMenu, null, customServerItem);
 		};
-		
+
 		// Ensure the menu is populated (every time the parent menu is opened)
 		browseServerMenu.getParentMenu().setOnShowing(validationHandler);	
 		return browseServerMenu;
 	}
+
+  private static List<String> getServerList(StringProperty usedServerProp) {
+    Gson gson = new Gson();
+    List<String> usedServers = null;
+    try {
+        usedServers = gson.fromJson(usedServerProp.get(), new TypeToken<>() {});
+    } catch (JsonSyntaxException ignored) {}
+    if (usedServers == null) {
+      usedServers = new ArrayList<String>();
+    }
+    return usedServers;
+  }
+
+  static void handleLogin(QuPathGUI qupath, String path) {
+    try {
+      if (!path.startsWith("http:") && !path.startsWith("https:")) {
+        throw new IOException("The input URL must contain a scheme (e.g. \"https://\")!");
+      }
+      // Make the path a URI
+      URI uri = new URI(path);
+
+      // Clean the URI (in case it's a full path)
+      URI uriServer = OmeroTools.getServerURI(uri);
+
+      if (uriServer == null)
+        throw new MalformedURLException("Could not parse server from " + uri.toString());
+
+      // Check if client exist and if browser is already opened
+      var client = OmeroWebClients.getClientFromServerURI(uriServer);
+      if (client == null)
+        client = OmeroWebClients.createClientAndLogin(uriServer);
+
+      if (client == null)
+        throw new IOException("Could not parse server from " + uri.toString());
+
+      var browser = browsers.get(client);
+      if (browser == null || browser.getStage() == null) {
+        // Create new browser
+        browser = new OmeroWebImageServerBrowserCommand(qupath, client);
+        browsers.put(client, browser);
+        browser.run();
+      } else	// Request focus for already-existing browser
+        browser.getStage().requestFocus();		
+
+    } catch (FileNotFoundException ex) {
+      Dialogs.showErrorMessage("OMERO web server", String.format("An error occured when trying to reach %s: %s\"", path, ex.getLocalizedMessage()));
+    } catch (IOException | URISyntaxException ex) {
+      Dialogs.showErrorMessage("OMERO web server", ex.getLocalizedMessage());
+      return;
+    }
+  }
 
 	/**
 	 * Return map of currently opened browsers.
@@ -197,7 +252,7 @@ static Map<OmeroWebClient, OmeroWebImageServerBrowserCommand> getOpenedBrowsers(
 
 	@Override
 	public GitHubRepo getRepository() {
-		return GitHubRepo.create(getName(), "qupath", "qupath-extension-omero");
+		return GitHubRepo.create(getName(), "glencoesoftware", "qupath-extension-omero-web");
 	}
 
 	@Override