Fixed GitHub actions

qupath · Nov 7, 2023 · 867fbe3 · 867fbe3
1 parent 2c9ea7c
commit 867fbe3
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Showing 7 changed files with 37 additions and 49 deletions.
diff --git a/.github/workflows/build_jar.yml b/.github/workflows/build_jar.yml
@@ -17,6 +17,8 @@
          distribution: 'adopt-hotspot'
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
+     - name: Grant execute permission for OMERO server setup script
+       run: chmod +x src/test/resources/qupath/ext/omero/setupOmeroServer.sh
      - name: Build with Gradle
        run: ./gradlew build -P toolchain=11
      - uses: actions/upload-artifact@v2

diff --git a/.github/workflows/gradle.yml b/.github/workflows/gradle.yml
@@ -17,5 +17,7 @@
          distribution: 'adopt-hotspot'
      - name: Grant execute permission for gradlew
        run: chmod +x gradlew
+     - name: Grant execute permission for OMERO server setup script
+       run: chmod +x src/test/resources/qupath/ext/omero/setupOmeroServer.sh
      - name: Build with Gradle
        run: ./gradlew build -P toolchain=11
diff --git a/src/test/java/qupath/ext/omero/OmeroServer.java b/src/test/java/qupath/ext/omero/OmeroServer.java
@@ -112,8 +112,8 @@ protected void waitUntilReady() {
                             "/analysis.csv"
                     )
                     .withFileSystemBind(
-                            Objects.requireNonNull(OmeroServer.class.getResource("Dot_Blot.tif")).getPath(),
-                            "/Dot_Blot.tif"
+                            Objects.requireNonNull(OmeroServer.class.getResource("Cardio.tif")).getPath(),
+                            "/Cardio.tif"
                     )
                     .withFileSystemBind(
                             Objects.requireNonNull(OmeroServer.class.getResource("mitosis.tif")).getPath(),
@@ -309,33 +309,33 @@ protected static URI getImageURI() {
         return URI.create(getServerURL() + "/webclient/?show=image-" + getImage().getId());
     }
 
-    protected static String getImageAttributeValue(int informationIndex) {
+    protected static Image getOrphanedImage() {
+        return new Image(2);
+    }
+
+    protected static String getOrphanedImageAttributeValue(int informationIndex) {
         return switch (informationIndex) {
-            case 0 -> "mitosis.tif";
-            case 1 -> String.valueOf(getImage().getId());
+            case 0 -> "Cardio.tif";
+            case 1 -> String.valueOf(getOrphanedImage().getId());
             case 2 -> getCurrentOwner().getFullName();
             case 3 -> getCurrentGroup().getName();
             case 4, 13 -> "-";
-            case 5 -> "171 px";
-            case 6 -> "196 px";
-            case 7 -> "32.6 MB";
-            case 8 -> "5";
-            case 9 -> "2";
-            case 10 -> "51";
-            case 11, 12 -> "0.08850000022125 µm";
-            case 14 -> "uint16";
+            case 5 -> "1000 px";
+            case 6 -> "1000 px";
+            case 7 -> "2.9 MB";
+            case 8 -> "1";
+            case 9 -> "3";
+            case 10 -> "1";
+            case 11, 12 -> "-";
+            case 14 -> "uint8";
             default -> "";
         };
     }
 
-    protected static int getImageNumberOfAttributes() {
+    protected static int getOrphanedImageNumberOfAttributes() {
         return 15;
     }
 
-    protected static Image getOrphanedImage() {
-        return new Image(2);
-    }
-
     protected static List<Group> getGroups() {
         return List.of(
                 new Group(0, "system"),

diff --git a/...ava/qupath/ext/omero/core/entities/repositoryentities/serverentities/image/TestImage.java b/...ava/qupath/ext/omero/core/entities/repositoryentities/serverentities/image/TestImage.java
@@ -8,9 +8,8 @@
 import qupath.ext.omero.OmeroServer;
 import qupath.ext.omero.core.WebClient;
 import qupath.ext.omero.core.WebClients;
+import qupath.ext.omero.core.entities.repositoryentities.OrphanedFolder;
 import qupath.ext.omero.core.entities.repositoryentities.RepositoryEntity;
-import qupath.ext.omero.core.entities.repositoryentities.serverentities.Dataset;
-import qupath.ext.omero.core.entities.repositoryentities.serverentities.Project;
 
 import java.util.List;
 import java.util.concurrent.ExecutionException;
@@ -24,34 +23,19 @@ public class TestImage extends OmeroServer {
     static void createClient() throws ExecutionException, InterruptedException {
         client = OmeroServer.createValidClient();
 
-        while (client.getServer().isPopulatingChildren()) {
-            TimeUnit.MILLISECONDS.sleep(50);
-        }
-        Project project = client.getServer().getChildren().stream()
-                .filter(child -> child instanceof Project)
-                .map(p -> (Project) p)
-                .findAny()
-                .orElse(null);
-        assert project != null;
-
-        List<? extends RepositoryEntity> projectChildren = project.getChildren();
-        while (project.isPopulatingChildren()) {
-            TimeUnit.MILLISECONDS.sleep(50);
-        }
-
-        Dataset dataset = projectChildren.stream()
-                .filter(child -> child instanceof Dataset)
-                .map(d -> (Dataset) d)
+        OrphanedFolder orphanedFolder = client.getServer().getChildren().stream()
+                .filter(child -> child instanceof OrphanedFolder)
+                .map(p -> (OrphanedFolder) p)
                 .findAny()
                 .orElse(null);
-        assert dataset != null;
+        assert orphanedFolder != null;
 
-        List<? extends RepositoryEntity> datasetChildren = dataset.getChildren();
-        while (dataset.isPopulatingChildren()) {
+        List<? extends RepositoryEntity> orphanedFolderChildren = orphanedFolder.getChildren();
+        while (orphanedFolder.isPopulatingChildren()) {
             TimeUnit.MILLISECONDS.sleep(50);
         }
 
-        image = datasetChildren.stream()
+        image = orphanedFolderChildren.stream()
                 .filter(child -> child instanceof Image)
                 .map(d -> (Image) d)
                 .findAny()
@@ -86,10 +70,10 @@ void Check_Children() throws InterruptedException {
 
     @Test
     void Check_Attributes() {
-        int numberOfValues = OmeroServer.getImageNumberOfAttributes();
+        int numberOfValues = OmeroServer.getOrphanedImageNumberOfAttributes();
         String[] expectedAttributeValues = new String[numberOfValues];
         for (int i=0; i<numberOfValues; ++i) {
-            expectedAttributeValues[i] = OmeroServer.getImageAttributeValue(i);
+            expectedAttributeValues[i] = OmeroServer.getOrphanedImageAttributeValue(i);
         }
 
         String[] attributesValues = new String[numberOfValues];
@@ -102,7 +86,7 @@ void Check_Attributes() {
 
     @Test
     void Check_Number_Of_Attributes() {
-        int expectedNumberOfAttributes = OmeroServer.getImageNumberOfAttributes();
+        int expectedNumberOfAttributes = OmeroServer.getOrphanedImageNumberOfAttributes();
 
         int numberOfAttributes = image.getNumberOfAttributes();
 
@@ -117,16 +101,16 @@ void Check_Supported() {
     }
 
     @Test
-    void Check_Not_Uint8() {
+    void Check_Uint8() {
         boolean isUint8 = image.isUint8();
 
-        Assertions.assertFalse(isUint8);
+        Assertions.assertTrue(isUint8);
     }
 
     @Test
     void Check_Has_3_channels() {
         boolean has3Channels = image.has3Channels();
 
-        Assertions.assertFalse(has3Channels);
+        Assertions.assertTrue(has3Channels);
     }
 }
diff --git a/src/test/resources/qupath/ext/omero/Cardio.tif b/src/test/resources/qupath/ext/omero/Cardio.tif
diff --git a/src/test/resources/qupath/ext/omero/Dot_Blot.tif b/src/test/resources/qupath/ext/omero/Dot_Blot.tif
diff --git a/src/test/resources/qupath/ext/omero/setupOmeroServer.sh b/src/test/resources/qupath/ext/omero/setupOmeroServer.sh
@@ -16,6 +16,6 @@ file=$(/opt/omero/server/venv3/bin/omero obj new FileAnnotation file=$analysis)
 /opt/omero/server/venv3/bin/omero obj new Dataset name=orphaned_dataset
 
 /opt/omero/server/venv3/bin/omero import -d $dataset --transfer=ln_s /mitosis.tif
-/opt/omero/server/venv3/bin/omero import --transfer=ln_s /Dot_Blot.tif
+/opt/omero/server/venv3/bin/omero import --transfer=ln_s /Cardio.tif
 
 echo $analysis