From 95532cff2a299b8388441588f22728416691362e Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Tue, 17 Sep 2024 22:45:27 +0100 Subject: [PATCH 1/3] Use system proxy settings. The resolver for 'identifiers.org' uses the Apache HTTP client, which by default does not honor the JVM proxy settings. This commit updates the resolver to force the client to use said settings. closes #1231 --- .../editor/owl/model/identifiers/IdentifiersDotOrg.java | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/protege-editor-owl/src/main/java/org/protege/editor/owl/model/identifiers/IdentifiersDotOrg.java b/protege-editor-owl/src/main/java/org/protege/editor/owl/model/identifiers/IdentifiersDotOrg.java index 43b9ce497..9a9e3db9e 100644 --- a/protege-editor-owl/src/main/java/org/protege/editor/owl/model/identifiers/IdentifiersDotOrg.java +++ b/protege-editor-owl/src/main/java/org/protege/editor/owl/model/identifiers/IdentifiersDotOrg.java @@ -140,8 +140,6 @@ public List getCollections() { @Nonnull private static HttpClient createClient() { - return HttpClientBuilder.create().build(); - - + return HttpClientBuilder.create().useSystemProperties().build(); } } From 7b8f0cc34c70e2d4cff72a24fe71fa69746ec5b4 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 14 Aug 2024 22:35:03 +0100 Subject: [PATCH 2/3] Add persistence for the "show deprecated entities" option. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The setting of the "View > Show deprecated (obsolete) entities" menu option is not persistent and is always reset to its default value (false) whenever Protégé is started or a new ontology is open. This commit adds a new preference to store that setting so that it is made persistent. --- .../owl/model/hierarchy/ClassHierarchyPreferences.java | 10 ++++++++++ .../owl/ui/action/DisplayDeprecatedEntitiesAction.java | 4 +++- .../view/AbstractOWLEntityHierarchyViewComponent.java | 6 ++++-- 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/protege-editor-owl/src/main/java/org/protege/editor/owl/model/hierarchy/ClassHierarchyPreferences.java b/protege-editor-owl/src/main/java/org/protege/editor/owl/model/hierarchy/ClassHierarchyPreferences.java index c672e5ee6..adf4e5f4a 100644 --- a/protege-editor-owl/src/main/java/org/protege/editor/owl/model/hierarchy/ClassHierarchyPreferences.java +++ b/protege-editor-owl/src/main/java/org/protege/editor/owl/model/hierarchy/ClassHierarchyPreferences.java @@ -16,6 +16,8 @@ public class ClassHierarchyPreferences { private static final String DISPLAY_RELATIONSHIPS_KEY = "DISPLAY_RELATIONSHIPS"; + private static final String DISPLAY_DEPRECATED_ENTITIES_KEY = "DISPLAY_DEPRECATED_ENTITIES"; + private static Preferences getPreferences() { return PreferencesManager.getInstance().getApplicationPreferences(CLASS_HIERARCHY_PREFERENCES); } @@ -31,4 +33,12 @@ public boolean isDisplayRelationships() { public void setDisplayRelationships(boolean displayRelationships) { getPreferences().putBoolean(DISPLAY_RELATIONSHIPS_KEY, displayRelationships); } + + public boolean isDisplayDeprecatedEntities() { + return getPreferences().getBoolean(DISPLAY_DEPRECATED_ENTITIES_KEY, false); + } + + public void setDisplayDeprecatedEntities(boolean displayDeprecatedEntities) { + getPreferences().putBoolean(DISPLAY_DEPRECATED_ENTITIES_KEY, displayDeprecatedEntities); + } } diff --git a/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/DisplayDeprecatedEntitiesAction.java b/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/DisplayDeprecatedEntitiesAction.java index 9a27e4524..ece6fc282 100644 --- a/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/DisplayDeprecatedEntitiesAction.java +++ b/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/action/DisplayDeprecatedEntitiesAction.java @@ -1,5 +1,6 @@ package org.protege.editor.owl.ui.action; +import org.protege.editor.owl.model.hierarchy.ClassHierarchyPreferences; import org.protege.editor.owl.ui.view.HasDisplayDeprecatedEntities; import java.awt.event.ActionEvent; @@ -13,7 +14,7 @@ public class DisplayDeprecatedEntitiesAction extends ComponentHierarchyAction initialiseAction() { - putValue(SELECTED_KEY, false); + putValue(SELECTED_KEY, ClassHierarchyPreferences.get().isDisplayDeprecatedEntities()); return HasDisplayDeprecatedEntities.class; } @@ -21,5 +22,6 @@ protected Class initialiseAction() { protected void actionPerformedOnTarget(ActionEvent e, HasDisplayDeprecatedEntities target) { boolean value = (boolean) getValue(SELECTED_KEY); target.setShowDeprecatedEntities(value); + ClassHierarchyPreferences.get().setDisplayDeprecatedEntities(value); } } diff --git a/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/AbstractOWLEntityHierarchyViewComponent.java b/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/AbstractOWLEntityHierarchyViewComponent.java index feeb90d07..f3609b11d 100644 --- a/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/AbstractOWLEntityHierarchyViewComponent.java +++ b/protege-editor-owl/src/main/java/org/protege/editor/owl/ui/view/AbstractOWLEntityHierarchyViewComponent.java @@ -6,6 +6,7 @@ import org.protege.editor.core.ui.view.ViewMode; import org.protege.editor.core.util.HandlerRegistration; import org.protege.editor.owl.model.OWLModelManager; +import org.protege.editor.owl.model.hierarchy.ClassHierarchyPreferences; import org.protege.editor.owl.model.hierarchy.OWLObjectHierarchyProvider; import org.protege.editor.owl.ui.OWLObjectComparatorAdapter; import org.protege.editor.owl.ui.action.AbstractOWLTreeAction; @@ -170,8 +171,9 @@ public void mouseReleased(MouseEvent e) { breadCrumbTrailProviderRegistration = getOWLWorkspace().registerBreadcrumbTrailProvider(this); - // Don't show deprecated entities by default - getHierarchyProvider().setFilter(this::isNotDeprecated); + if (!ClassHierarchyPreferences.get().isDisplayDeprecatedEntities()) { + getHierarchyProvider().setFilter(this::isNotDeprecated); + } } private void scrollSelectedPathToVisibleRect() { From 888ad819516d48744cb61489bd45772d21396bb7 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 18 Sep 2024 10:10:39 +0100 Subject: [PATCH 3/3] Switch GA workflows to use the Temurin JDK. The maintainers of the 'setup-java' GitHub Action recommends migrating from 'adopt' to 'temurin' [1], given that "AdoptOpenJDK got moved to Eclipse Temurin and won't be updated anymore". [1] https://github.com/actions/setup-java --- .github/workflows/ci.yml | 2 +- .github/workflows/publish.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2a0bf267a..7a91ce699 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,6 +19,6 @@ jobs: uses: actions/setup-java@v4 with: java-version: '11' - distribution: 'adopt' + distribution: 'temurin' - name: Run test suite run: mvn --batch-mode --activate-profiles ${{ matrix.profile }} --define release.signing.disabled=true clean verify diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 05dbe5d3c..057ecdb0b 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -14,7 +14,7 @@ jobs: uses: actions/setup-java@v4 with: java-version: '11' - distribution: 'adopt' + distribution: 'temurin' server-id: ossrh server-username: OSSRH_USERNAME server-password: OSSRH_TOKEN