Added ICE tests

qupath · Nov 13, 2023 · 9acacc0 · 9acacc0
1 parent 7e8e232
commit 9acacc0
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Showing 15 changed files with 142 additions and 76 deletions.
diff --git a/src/main/java/qupath/ext/omero/core/WebClient.java b/src/main/java/qupath/ext/omero/core/WebClient.java
@@ -171,13 +171,6 @@ public ReadOnlyStringProperty getUsername() {
         return username;
     }
 
-    /**
-     * @return the base URI of the server
-     */
-    public URI getServerURI() {
-        return apisHandler.getHost();
-    }
-
     public ObjectProperty<PixelAPI> getSelectedPixelAPI() {
         return selectedPixelAPI;
     }

diff --git a/src/main/java/qupath/ext/omero/core/WebClients.java b/src/main/java/qupath/ext/omero/core/WebClients.java
@@ -56,7 +56,7 @@ public static CompletableFuture<WebClient> createClient(String url, String... ar
 
             return existingClient.map(CompletableFuture::completedFuture).orElseGet(() -> WebClient.create(serverURI.get(), args).thenApply(client -> {
                 if (client.getStatus().equals(WebClient.Status.SUCCESS)) {
-                    ClientsPreferencesManager.addURI(client.getServerURI().toString());
+                    ClientsPreferencesManager.addURI(client.getApisHandler().getWebServerURI().toString());
                     updateClients(client, Operation.ADD);
                 }
                 return client;
@@ -87,7 +87,7 @@ public static WebClient createClientSync(String url, String... args) {
             if (existingClient.isEmpty()) {
                 var client = WebClient.createSync(serverURI.get(), args);
                 if (client.getStatus().equals(WebClient.Status.SUCCESS)) {
-                    ClientsPreferencesManager.addURI(client.getServerURI().toString());
+                    ClientsPreferencesManager.addURI(client.getApisHandler().getWebServerURI().toString());
                     updateClients(client, Operation.ADD);
                 }
 
@@ -142,6 +142,6 @@ private static Optional<URI> getServerURI(String url) {
     }
 
     private static Optional<WebClient> getExistingClient(URI uri) {
-        return clients.stream().filter(e -> e.getServerURI().equals(uri)).findAny();
+        return clients.stream().filter(e -> e.getApisHandler().getWebServerURI().equals(uri)).findAny();
     }
 }
diff --git a/src/main/java/qupath/ext/omero/core/apis/ApisHandler.java b/src/main/java/qupath/ext/omero/core/apis/ApisHandler.java
@@ -108,17 +108,17 @@ public WebClient getClient() {
     }
 
     /**
-     * @return the base server URI (e.g. <a href="https://idr.openmicroscopy.org">https://idr.openmicroscopy.org</a>)
+     * @return the web server URI (e.g. <a href="https://idr.openmicroscopy.org">https://idr.openmicroscopy.org</a>)
      */
-    public URI getHost() {
+    public URI getWebServerURI() {
         return host;
     }
 
     /**
-     * See {@link JsonApi#getHost()}.
+     * See {@link JsonApi#getServerURI()}.
      */
-    public String getServerHost() {
-        return jsonApi.getHost();
+    public String getServerURI() {
+        return jsonApi.getServerURI();
     }
 
     /**

diff --git a/src/main/java/qupath/ext/omero/core/apis/JsonApi.java b/src/main/java/qupath/ext/omero/core/apis/JsonApi.java
@@ -99,10 +99,22 @@ public String getToken() {
     }
 
     /**
-     * @return the server host of this server. This is the OMERO server
-     * host and may be different from the OMERO web host
+     * <p>
+     *     Get the server URI of this server. This is the <b>OMERO server</b>
+     *     URI and may be different from the <b>OMERO web</b> URI.
+     * </p>
+     * <p>
+     *     The returned address is the address used by OMERO web to communicate
+     *     with an OMERO server. If these two entities are running on the same server,
+     *     the returned value of this function may be {@code localhost} or any local IP.
+     *     Therefore, if you can't communicate with the returned value of this function,
+     *     you should be able to communicate with the address of OMERO web (returned by
+     *     {@link ApisHandler#getWebServerURI()}.
+     * </p>
+     *
+     * @return the server host
      */
-    public String getHost() {
+    public String getServerURI() {
         return serverHost;
     }
 

diff --git a/src/main/java/qupath/ext/omero/core/pixelapis/ice/IceAPI.java b/src/main/java/qupath/ext/omero/core/pixelapis/ice/IceAPI.java
@@ -19,7 +19,7 @@ public class IceAPI implements PixelAPI {
 
     private static final Logger logger = LoggerFactory.getLogger(IceAPI.class);
     static final String NAME = "Ice";
-    private static Boolean gatewayAvailable;
+    private static boolean gatewayAvailable;
     private final WebClient client;
 
     static {
@@ -98,6 +98,6 @@ public PixelAPIReader createReader(
 
     @Override
     public String toString() {
-        return String.format("Ice API of %s", client.getServerURI());
+        return String.format("Ice API of %s", client.getApisHandler().getWebServerURI());
     }
 }
diff --git a/src/main/java/qupath/ext/omero/core/pixelapis/ice/IceReader.java b/src/main/java/qupath/ext/omero/core/pixelapis/ice/IceReader.java
@@ -12,6 +12,7 @@
 import omero.gateway.model.PixelsData;
 import omero.model.ExperimenterGroup;
 import qupath.ext.omero.core.WebClient;
+import qupath.ext.omero.core.apis.ApisHandler;
 import qupath.lib.color.ColorModelFactory;
 import qupath.lib.images.servers.ImageChannel;
 import qupath.lib.images.servers.PixelType;
@@ -32,7 +33,7 @@
  */
 class IceReader implements PixelAPIReader {
 
-    private final Gateway gateway;
+    private final Gateway gateway = new Gateway(new IceLogger());
     private final RawPixelsStorePrx reader;
     private final int numberOfResolutionLevels;
     private final int nChannels;
@@ -52,13 +53,7 @@ class IceReader implements PixelAPIReader {
      */
     public IceReader(WebClient client, long imageID, List<ImageChannel> channels) throws IOException {
         try {
-            gateway = new Gateway(new IceLogger());
-            ExperimenterData user = gateway.connect(new LoginCredentials(
-                    client.getUsername().get(),
-                    client.getPassword().map(String::valueOf).orElse(null),
-                    client.getApisHandler().getServerHost(),
-                    client.getApisHandler().getPort()
-            ));
+            ExperimenterData user = connect(client);
 
             context = new SecurityContext(user.getGroupId());
 
@@ -145,6 +140,35 @@ public String toString() {
         return String.format("Ice reader for %s", context.getServerInformation());
     }
 
+    /**
+     * Attempt to create a connection with the server. The OMERO web host will be
+     * used, and if not successful, the OMERO server host will be used (see
+     * {@link ApisHandler#getServerURI()}).
+     *
+     * @param client  the connection to use
+     * @return a valid connection
+     * @throws DSOutOfServiceException when a connection cannot be established
+     */
+    private ExperimenterData connect(WebClient client) throws DSOutOfServiceException {
+        try {
+            return gateway.connect(new LoginCredentials(
+                    client.getUsername().get(),
+                    client.getPassword().map(String::valueOf).orElse(null),
+                    client.getApisHandler().getWebServerURI().getHost(),
+                    client.getApisHandler().getPort()
+            ));
+        } catch (DSOutOfServiceException e) {
+            System.err.println(client.getApisHandler().getWebServerURI().toString());
+
+            return gateway.connect(new LoginCredentials(
+                    client.getUsername().get(),
+                    client.getPassword().map(String::valueOf).orElse(null),
+                    client.getApisHandler().getServerURI(),
+                    client.getApisHandler().getPort()
+            ));
+        }
+    }
+
     private Optional<ImageData> getImage(long imageID) throws ExecutionException, DSOutOfServiceException, ServerError {
         BrowseFacility browser = gateway.getFacility(BrowseFacility.class);
         try {

diff --git a/src/main/java/qupath/ext/omero/core/pixelapis/web/WebAPI.java b/src/main/java/qupath/ext/omero/core/pixelapis/web/WebAPI.java
@@ -88,6 +88,6 @@ public PixelAPIReader createReader(
 
     @Override
     public String toString() {
-        return String.format("Web API of %s", client.getServerURI());
+        return String.format("Web API of %s", client.getApisHandler().getWebServerURI());
     }
 }
diff --git a/src/main/java/qupath/ext/omero/gui/browser/BrowseMenu.java b/src/main/java/qupath/ext/omero/gui/browser/BrowseMenu.java
@@ -73,7 +73,7 @@ private void setUpListeners() {
             for (WebClient client: change.getList()) {
                 BrowserCommand browserCommand = getBrowserCommand(client);
 
-                MenuItem clientMenuItem = new MenuItem(client.getServerURI() + "...");
+                MenuItem clientMenuItem = new MenuItem(client.getApisHandler().getWebServerURI() + "...");
                 clientMenuItem.setOnAction(e -> browserCommand.run());
                 getItems().add(clientMenuItem);
             }

diff --git a/src/main/java/qupath/ext/omero/gui/browser/serverbrowser/Browser.java b/src/main/java/qupath/ext/omero/gui/browser/serverbrowser/Browser.java
@@ -236,7 +236,7 @@ private void onImportButtonClicked(ActionEvent ignoredEvent) {
     }
 
     private void initUI() {
-        serverHost.setText(client.getServerURI().getHost());
+        serverHost.setText(client.getApisHandler().getWebServerURI().getHost());
 
         if (client.getSelectedPixelAPI().get().canAccessRawPixels()) {
             rawPixelAccess.setText(resources.getString("Browser.Browser.accessRawPixels"));

diff --git a/src/main/java/qupath/ext/omero/gui/connectionsmanager/ConnectionsManager.java b/src/main/java/qupath/ext/omero/gui/connectionsmanager/ConnectionsManager.java
@@ -87,6 +87,6 @@ private void populate() {
     }
 
     private static boolean clientWithURIExists(String uri) {
-        return ConnectionsManagerModel.getClients().stream().anyMatch(client -> client.getServerURI().toString().equals(uri));
+        return ConnectionsManagerModel.getClients().stream().anyMatch(client -> client.getApisHandler().getWebServerURI().toString().equals(uri));
     }
 }
diff --git a/src/main/java/qupath/ext/omero/gui/connectionsmanager/connection/Connection.java b/src/main/java/qupath/ext/omero/gui/connectionsmanager/connection/Connection.java
@@ -66,7 +66,7 @@ public class Connection extends VBox {
      * @throws IOException if an error occurs while creating the pane
      */
     public Connection(WebClient client) throws IOException {
-        this(client, client.getServerURI().toString());
+        this(client, client.getApisHandler().getWebServerURI().toString());
     }
 
     /**
@@ -141,7 +141,7 @@ private void onConnectionClicked(ActionEvent ignoredEvent) {
                                 resources.getString("ConnectionsManager.Connection.login"),
                                 MessageFormat.format(
                                         resources.getString("ConnectionsManager.Connection.loginSuccessful"),
-                                        client.getServerURI(),
+                                        client.getApisHandler().getWebServerURI(),
                                         client.getUsername().get()
                                 )
                         );

diff --git a/src/test/java/qupath/ext/omero/OmeroServer.java b/src/test/java/qupath/ext/omero/OmeroServer.java
@@ -53,15 +53,13 @@ public abstract class OmeroServer {
     private static final int CLIENT_CREATION_ATTEMPTS = 3;
     private static final String OMERO_PASSWORD = "password";
     private static final int OMERO_SERVER_PORT = 4064;
+    private static final boolean dockerAvailable = DockerClientFactory.instance().isDockerAvailable();
     private static final GenericContainer<?> postgres;
     private static final GenericContainer<?> omeroServer;
     private static final GenericContainer<?> omeroWeb;
-    private static final boolean dockerAvailable;
     private static final String analysisFileId;
 
     static {
-        dockerAvailable = DockerClientFactory.instance().isDockerAvailable();
-
         if (!dockerAvailable || IS_LOCAL_OMERO_SERVER_RUNNING) {
             postgres = null;
             omeroServer = null;

diff --git a/src/test/java/qupath/ext/omero/core/TestWebClient.java b/src/test/java/qupath/ext/omero/core/TestWebClient.java
@@ -37,15 +37,6 @@ void Check_Client_Username() {
         Assertions.assertEquals(expectedUsername, username);
     }
 
-    @Test
-    void Check_Client_URI() {
-        URI expectedURI = URI.create(OmeroServer.getServerURL());
-
-        URI uri = client.getServerURI();
-
-        Assertions.assertEquals(expectedURI, uri);
-    }
-
     @Test
     void Check_Opened_Images_When_One_Image_Added() {
         int expectedSize = client.getOpenedImagesURIs().size() + 1;

diff --git a/src/test/java/qupath/ext/omero/core/apis/TestApisHandler.java b/src/test/java/qupath/ext/omero/core/apis/TestApisHandler.java
@@ -52,7 +52,7 @@ static void removeClient() {
     void Check_Host() {
         URI expectedHost = URI.create(OmeroServer.getServerURL());
 
-        URI host = apisHandler.getHost();
+        URI host = apisHandler.getWebServerURI();
 
         Assertions.assertEquals(expectedHost, host);
     }
@@ -61,7 +61,7 @@ void Check_Host() {
     void Check_Server_Host() {
         String expectedServerHost = OmeroServer.getServerHost();
 
-        String serverHost = apisHandler.getServerHost();
+        String serverHost = apisHandler.getServerURI();
 
         Assertions.assertEquals(expectedServerHost, serverHost);
     }