Enable JDK-EA builds again #13036

koppor · 2025-04-30T10:47:37Z

Experiments based on #13033 - not pushing to #13033, do avoid noice for the contributor.

With this PR, we are working towards having a single mise.toml configuring the JDK. Works for all GitHub workflows; need to update IDE instructions (there is a mise plugin) - and look at the dev container etc.

Howto for windows:

mise install (in JabRef dir)
Copy %APPDATA%\..\Local\mise\installs\* to c:\user\{login}\.asdf\installs\*. - see Add support for mise locations. gradle/foojay-toolchains#110
Install Mise IntelliJ Plugin
Update code howto that both JDK21 (for gradle) and other JDK is found

Kind of blocker: 134130/intellij-mise#234

Mandatory checks

I own the copyright of the code submitted and I license it under the MIT license
[.] Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
[.] Tests created for changes (if applicable)
[.] Manually tested changed features in running JabRef (always required)
[.] Screenshots added in PR description (if change is visible to the user)
[.] Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
[.] Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

…project build directory

koppor · 2025-04-30T11:47:30Z

Underlying exception : org.mockito.exceptions.base.MockitoException: Could not modify all classes [class java.lang.Object, class org.jabref.logic.bibtex.FieldPreferences]
        at app//org.jabref.logic.shared.SynchronizationSimulatorTest.setup(SynchronizationSimulatorTest.java:56)

        Caused by:
        org.mockito.exceptions.base.MockitoException: Could not modify all classes [class java.lang.Object, class org.jabref.logic.bibtex.FieldPreferences]
            at app//net.bytebuddy.TypeCache.findOrInsert(TypeCache.java:168)
            at app//net.bytebuddy.TypeCache$WithInlineExpunction.findOrInsert(TypeCache.java:399)
            at app//net.bytebuddy.TypeCache.findOrInsert(TypeCache.java:190)
            at app//net.bytebuddy.TypeCache$WithInlineExpunction.findOrInsert(TypeCache.java:410)
            ... 1 more

            Caused by:
            java.lang.IllegalStateException: 
            Byte Buddy could not instrument all classes within the mock's type hierarchy

            This problem should never occur for javac-compiled classes. This problem has been observed for classes that are:
             - Compiled by older versions of scalac
             - Classes that are part of the Android distribution
                at org.mockito.internal.creation.bytebuddy.InlineBytecodeGenerator.triggerRetransformation(InlineBytecodeGenerator.java:291)
                at org.mockito.internal.creation.bytebuddy.InlineBytecodeGenerator.mockClass(InlineBytecodeGenerator.java:220)
                at org.mockito.internal.creation.bytebuddy.TypeCachingBytecodeGenerator.lambda$mockClass$0(TypeCachingBytecodeGenerator.java:78)
                at net.bytebuddy.TypeCache.findOrInsert(TypeCache.java:168)
                at net.bytebuddy.TypeCache$WithInlineExpunction.findOrInsert(TypeCache.java:399)
                at net.bytebuddy.TypeCache.findOrInsert(TypeCache.java:190)
                at net.bytebuddy.TypeCache$WithInlineExpunction.findOrInsert(TypeCache.java:410)
                at org.mockito.internal.creation.bytebuddy.TypeCachingBytecodeGenerator.mockClass(TypeCachingBytecodeGenerator.java:75)
                at org.mockito.internal.creation.bytebuddy.InlineDelegateByteBuddyMockMaker.createMockType(InlineDelegateByteBuddyMockMaker.java:429)
                at org.mockito.internal.creation.bytebuddy.InlineDelegateByteBuddyMockMaker.doCreateMock(InlineDelegateByteBuddyMockMaker.java:388)
                at org.mockito.internal.creation.bytebuddy.InlineDelegateByteBuddyMockMaker.createMock(InlineDelegateByteBuddyMockMaker.java:367)
                at org.mockito.internal.creation.bytebuddy.InlineByteBuddyMockMaker.createMock(InlineByteBuddyMockMaker.java:56)
                at org.mockito.internal.util.MockUtil.createMock(MockUtil.java:99)
                at org.mockito.internal.MockitoCore.mock(MockitoCore.java:84)
                at org.mockito.Mockito.mock(Mockito.java:2198)
                at org.mockito.Mockito.mock(Mockito.java:2113)
                ... 1 more

                Caused by:
                java.lang.IllegalArgumentException: Java 25 (69) is not supported by the current version of Byte Buddy which officially supports Java 24 (68) - update Byte Buddy or set net.bytebuddy.experimental as a VM property

koppor · 2025-04-30T11:57:21Z

Updated bytebuddy to latest version to support JDK25: https://github.com/raphw/byte-buddy/releases/tag/byte-buddy-1.17.5

Siedlerchr · 2025-04-30T12:13:16Z

jmod module path on mac is wrong, uses/evaluates to --module-path /Users/runner/hostedtoolcache/Java_Temurin-Hotspot_jdk/21.0.7-6.0/arm64/Contents/Home/jmods/:build/jlinkbase/jlinkjars \

koppor · 2025-04-30T12:40:16Z

Windows:

> Could not copy file 'D:\a\jabref\jabref\jabgui\buildres\windows\JabRef-post-image.wsf' to 'D:\a\jabref\jabref\jabgui\build\jpackage-resource-dir\JabRef-post-image.wsf'.
You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins.
   > Error - Invalid filter specification for org.apache.tools.ant.filters.ReplaceTokens

koppor · 2025-04-30T13:02:21Z

Windows:

[12:56:51.506] java.io.IOException: Command [cscript, D:\a\jabref\jabref\jabgui\build\installer\config\JabRef-post-image.wsf] in D:\a\jabref\jabref\jabgui\build\installer\images\win-msi.image exited with 1 code
	at jdk.jpackage/jdk.jpackage.internal.Executor.executeExpectSuccess(Executor.java:90)
	at jdk.jpackage/jdk.jpackage.internal.ScriptRunner.run(ScriptRunner.java:100)
	at jdk.jpackage/jdk.jpackage.internal.WinMsiBundler.execute(WinMsiBundler.java:440)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.executeBundler(Arguments.java:740)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.generateBundle(Arguments.java:701)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.processArguments(Arguments.java:552)
	at jdk.jpackage/jdk.jpackage.main.Main.execute(Main.java:93)
	at jdk.jpackage/jdk.jpackage.main.Main.main(Main.java:54)
[12:56:51.507] Kept working directory for debug: D:\a\jabref\jabref\jabgui\build\installer
[12:56:51.507] jdk.jpackage.internal.model.PackagerException: java.io.IOException: Command [cscript, D:\a\jabref\jabref\jabgui\build\installer\config\JabRef-post-image.wsf] in D:\a\jabref\jabref\jabgui\build\installer\images\win-msi.image exited with 1 code
	at jdk.jpackage/jdk.jpackage.internal.WinMsiBundler.execute(WinMsiBundler.java:445)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.executeBundler(Arguments.java:740)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.generateBundle(Arguments.java:701)
	at jdk.jpackage/jdk.jpackage.internal.Arguments.processArguments(Arguments.java:552)
	at jdk.jpackage/jdk.jpackage.main.Main.execute(Main.java:93)
	at jdk.jpackage/jdk.jpackage.main.Main.main(Main.java:54)
Caused by: java.io.IOException: Command [cscript, D:\a\jabref\jabref\jabgui\build\installer\config\JabRef-post-image.wsf] in D:\a\jabref\jabref\jabgui\build\installer\images\win-msi.image exited with 1 code
	at jdk.jpackage/jdk.jpackage.internal.Executor.executeExpectSuccess(Executor.java:90)
	at jdk.jpackage/jdk.jpackage.internal.ScriptRunner.run(ScriptRunner.java:100)
	at jdk.jpackage/jdk.jpackage.internal.WinMsiBundler.execute(WinMsiBundler.java:440)
	... 5 more

Siedlerchr · 2025-04-30T13:06:26Z

.github/workflows/deployment.yml

@@ -126,6 +141,8 @@ jobs:
          set -e
          cd jabgui

+          eval "$(mise hook-env)"
+


seems like the env.JAVA_HOME var is not set correctly
jlink failed with: Error: jlink version 25.0 does not match target java.base version 21.0

jdx/mise#4973

…ge-update-to-JDK25

koppor · 2025-05-01T20:41:35Z

Too much effort; we will "just" use JDK25 as soon as it is released.

github-actions · 2025-05-01T20:41:49Z

The build for this PR is no longer available. Please visit https://builds.jabref.org/main/ for the latest build.

…ge-update-to-JDK25

…JabRef/jabref into fix-jpackage-post-image-update-to-JDK25

.github/workflows/deployment-ea.yml

+          --java-options --add-opens=javafx.base/javafx.collections.transformation=org.jabref \
+          --java-options --add-modules=jdk.incubator.vector
+
+          # Add additional files / directories
+          cp buildres/mac/jabrefHost.py build/distribution/JabRef.app/Contents/
+          cp -R buildres/mac/native-messaging-host build/distribution/JabRef.app/Contents/
+
+          # Sign the final artifact
+          codesign --force --deep --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" \
+            --entitlements buildres/mac/jabref.entitlements \
+            --options runtime --timestamp build/distribution/JabRef.app
+
+          # pack dmg and pkg
+          hdiutil create -volname "JabRef" -srcfolder build/distribution/JabRef.app -ov -format UDZO build/distribution/JabRef${{ matrix.suffix }}.dmg
+          productbuild --component build/distribution/JabRef.app /Applications --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" build/distribution/JabRef${{ matrix.suffix }}.pkg
+
+          # Cleanup unpacked file
+          rm -rf build/distribution/JabRef.app
+      - name: Build runtime image and installer (linux, Windows)
+        if: (matrix.os != 'macos-13') && (matrix.os != 'macos-14') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabgui:jpackage
+      - name: Build JabKit
+        if: (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" :jabkit:jpackage
+      - name: Remove JabKit build for macOS
+        if: (matrix.os == 'macos-13') || (matrix.os == 'macos-14')
+        run: rm -rf jabkit/build/distribution/jabkit.app
+      - name: Package application image (linux, Windows)
+        if: (matrix.os != 'macos-13') && (matrix.os != 'macos-14') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: |
+          set -e
+          ${{ matrix.archivePortable }}
+          ${{ matrix.archivePortableJabKit }}
+      - name: Rename files
+        if: (matrix.os != 'macos-13') && (matrix.os != 'macos-14') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: pwsh
+        run: |
+          get-childitem -Path jabgui/build/distribution/* | rename-item -NewName {$_.name -replace "${{ steps.gitversion.outputs.AssemblySemVer }}","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}"}
+          get-childitem -Path jabgui/build/distribution/* | rename-item -NewName {$_.name -replace "portable","${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-portable"}
+      - name: Repack deb file for Debian
+        if: (matrix.os == 'ubuntu-22.04') && (steps.checksecrets.outputs.secretspresent == 'YES')
+        shell: bash
+        run: |
+          cd jabgui/build/distribution
+          ar x jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
+          zstd -d < control.tar.zst | xz > control.tar.xz
+          zstd -d < data.tar.zst | xz > data.tar.xz
+          ar -m -c -a sdsd jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb debian-binary control.tar.xz data.tar.xz
+          rm debian-binary control.tar.* data.tar.*
+          mv -f jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64_repackaged.deb jabref_${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}_amd64.deb
+      - name: Setup rsync (macOS)
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && (((matrix.os == 'macos-13') || (matrix.os == 'macos-14')) && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true))) }}
+        run: brew install rsync
+      - name: Setup rsync (Windows)
+        if: (matrix.os == 'windows-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        # We want to have rsync available at this place to avoid uploading and downloading from GitHub artifact store (taking > 5 minutes in total)
+        # We cannot use "action-rsyncer", because that requires Docker which is unavailable on Windows
+        # We cannot use "setup-rsync", because that does not work on Windows
+        # We do not use egor-tensin/setup-cygwin@v4, because it replaces the default shell
+        run: choco install --no-progress rsync
+      - name: Setup SSH key
+        if: ${{ (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (!((startsWith(github.ref, 'refs/tags/') || (inputs.notarization == true)))) }}
+        run: |
+          echo "${{ secrets.buildJabRefPrivateKey }}" > sshkey
+          chmod 600 sshkey
+      - name: Upload to builds.jabref.org (Windows)
+        if: (matrix.os == 'windows-latest') && (steps.checksecrets.outputs.secretspresent == 'YES') && (!startsWith(github.ref, 'refs/heads/gh-readonly-queue'))
+        shell: cmd
+        # for rsync installed by chocolatey, we need the ssh.exe delivered with that installation
+        run: |
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabgui/build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'C:\ProgramData\chocolatey\lib\rsync\tools\bin\ssh.exe -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+      - name: Upload to builds.jabref.org (linux, macOS)
+        # macOS: Negated condition of "Upload to GitHub workflow artifacts store (macOS)"
+        #        Reason: We either upload the non-notarized files - or notarize the files later (and upload these later)
+        # needs to be on one line; multi line does not work
+        if: ${{ (!startsWith(github.ref, 'refs/heads/gh-readonly-queue')) && (steps.checksecrets.outputs.secretspresent == 'YES') && ((matrix.os == 'ubuntu-22.04') || (matrix.os == 'macos-13') || (matrix.os == 'macos-14')) && !((startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)) }}
+        shell: bash
+        run: |
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabgui/build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+          rsync -rt --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r --itemize-changes --stats --rsync-path="mkdir -p /var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }} && rsync" -e 'ssh -p 9922 -i sshkey -o StrictHostKeyChecking=no' jabkit/build/distribution/ jrrsync@build-upload.jabref.org:/var/www/builds.jabref.org/www/${{ steps.gitversion.outputs.branchName }}/ || true
+      - name: Upload to GitHub workflow artifacts store (macOS)
+        if: ((matrix.os == 'macos-13')  || (matrix.os == 'macos-14')) && (steps.checksecrets.outputs.secretspresent == 'YES') && (startsWith(github.ref, 'refs/tags/') || inputs.notarization == true)
+        uses: actions/upload-artifact@v4
+        with:
+          # tbn = to-be-notarized
+          name: JabRef-macOS-tbn-${{ matrix.os }}
+          path: build/distribution
+          compression-level: 0 # no compression
+      - name: Upload to GitHub workflow artifacts store
+        if: (steps.checksecrets.outputs.secretspresent != 'YES')
+        uses: actions/upload-artifact@v4
+        with:
+          name: JabRef-${{ matrix.os }}
+          path: build/distribution
+          compression-level: 0 # no compression
+  announce:


To fix the issue, we will add a permissions block at the root level of the workflow to define the minimal permissions required for the GITHUB_TOKEN. Based on the workflow's operations, the contents: read permission is sufficient for most steps, as it allows the workflow to read repository contents without granting unnecessary write access. If specific jobs or steps require additional permissions, they can be defined at the job level.

.github/workflows/deployment-ea.yml

+    name: Comment on pull request
+    runs-on: ubuntu-22.04
+    needs: [build]
+    if: ${{ github.event_name == 'pull_request' }}
+    steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
+            echo "❌ Secret BUILDJABREFPRIVATEKEY not present"
+          else
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
+            echo "✔️ Secret BUILDJABREFPRIVATEKEY present"
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Comment PR
+        if: (steps.checksecrets.outputs.secretspresent == 'YES')
+        uses: thollander/actions-comment-pull-request@v3
+        with:
+          message: |
+            The build of this PR is available at <https://builds.jabref.org/pull/${{ github.event.pull_request.number }}/merge>.
+          comment-tag: download-link
+          mode: recreate
+  notarize: # outsourced in a separate job to be able to rerun if this fails for timeouts


To fix the issue, we will add a permissions block to the announce job to explicitly define the minimal permissions required. Since the job interacts with pull requests by adding comments, it needs pull-requests: write. All other permissions will be omitted to restrict access.

.github/workflows/deployment-ea.yml

trag-bot · 2025-05-04T18:36:26Z

@trag-bot didn't find any issues in the code! ✅✨

koppor · 2025-05-04T18:51:16Z

Closing, because too much back and forth - will start a clean PR - which "just" enables -ea builds.

alexeysemenyukoracle and others added 11 commits April 29, 2025 12:28

Fix JabRef-post-image.wsf to make it agnostic to the location of the …

28be33f

…project build directory

move to jabgui

407af96

fix errors and convert to build dir from layout

65eb404

Use mise and JDK25-ea

aac904f

Fix path

222c9ae

Check if mise sets env vars

1a25775

Refine Java installation

f2b7e15

Fix path on Windows

37590f8

Use jdpackage from JDK25

33fc6c3

Use mise everywhere

bd76b44

Updating the gradle wrapper does not need any JDK

80baef8

Update byte-buddy

b943996

koppor added 5 commits April 30, 2025 14:44

More byte buddy

09c04a1

Try to set JAVA_HOME

8f804ea

Remove main.wxs

9289d93

Try quick hack for .kts

dc293db

Enable debugging OpenRewrite

f5859d7

Siedlerchr reviewed Apr 30, 2025

View reviewed changes

koppor added 7 commits April 30, 2025 15:16

Fix PATH and JAVA_HOME

35a5a58

Merge remote-tracking branch 'origin/main' into fix-jpackage-post-ima…

3bf0aae

…ge-update-to-JDK25

Fix brace

e9e7fbb

Fix typo

5d0a2b5

Fix path

2f4866a

Add some debug

bf4328e

More debug - and try to fix

71f7f3a

This was referenced Apr 30, 2025

Fix path - and fix typo #13038

Merged

Update docs to new structure #13039

Merged

koppor closed this May 1, 2025

Merge remote-tracking branch 'origin/main' into fix-jpackage-post-ima…

462b953

…ge-update-to-JDK25

koppor reopened this May 4, 2025

koppor changed the title ~~Update to JDK25~~ Enable JDK-EA builds again May 4, 2025

koppor added 2 commits May 4, 2025 20:16

Discard changes to .github/workflows/tests.yml

4b19e64

Discard changes to .github/workflows/tests-fetchers.yml

d371a46

koppor mentioned this pull request May 4, 2025

Fix environment variable JAVA_HOME #13054

Merged

1 task

koppor added 6 commits May 4, 2025 20:23

Initial -jdk-ea version

793ed12

Discard changes to .github/workflows/deployment.yml

3173d43

Discard changes to mise.toml

ae52cce

Merge branch 'fix-jpackage-post-image-update-to-JDK25' of github.com:…

c2f4f5f

…JabRef/jabref into fix-jpackage-post-image-update-to-JDK25

Downgrad regular toolchain

a9b85bb

Try to update to JDK-ea using mise

cefcece

github-advanced-security bot found potential problems May 4, 2025

View reviewed changes

koppor closed this May 4, 2025

koppor mentioned this pull request May 4, 2025

Add -ea workflow (both JDK-ea and JavaFX-ea) #13056

Merged

1 task

koppor deleted the fix-jpackage-post-image-update-to-JDK25 branch May 11, 2025 15:01

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