Fix XMP write by koppor · Pull Request #8658 · JabRef/jabref

koppor · 2022-04-10T21:14:53Z

Follow-up to #8656 after feedback.

Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
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.

Additonally: Rename file -> path

ThiloteE · 2022-04-10T22:20:15Z

koppor · 2022-04-10T22:23:09Z

We need the hacky workarounds because of Apache PDF Box 3.0 limitations

Save the document to a file using default compression.
Don't use the input file as target as this will produce a corrupted file.

See https://issues.apache.org/jira/browse/PDFBOX-4028 for a discussion.

There is a warning output

Source code:

https://github.com/apache/pdfbox/blob/641efac28791f18f6afd6dee378911c4fa77710d/pdfbox/src/main/java/org/apache/pdfbox/pdmodel/PDDocument.java#L957

koppor · 2022-04-10T22:29:01Z

Some other programmers might also have issues with corrupt PDFs: https://stackoverflow.com/q/68904812/873282

koppor · 2022-04-10T22:32:43Z

Think, we need a log bridge for import org.apache.commons.logging.LogFactory;

koppor · 2022-04-10T22:54:00Z

I set this ready-for-review. I can undo the logging change if you want. See https://www.slf4j.org/legacy.html

I "hacked" with synchronized, but it works :)

Siedlerchr · 2022-04-11T04:40:30Z

The logging change results in method too large on windows

* upstream/main: Bump h2-mvstore from 2.1.210 to 2.1.212 in /buildSrc (#8665) Bump actions/setup-java from 2 to 3 (#8660) Bump hmarr/auto-approve-action from 2.2.0 to 2.2.1 (#8661) Bump unoloader from 7.3.0 to 7.3.2 (#8662) Bump antlr from 3.5.2 to 3.5.3 (#8663)

ThiloteE · 2022-04-11T16:30:50Z

Edit: Never mind. Had not downloaded newest changes on main branch yet. After I did that, no error. except the usual warning:

INFO: Index path for E:\server-ALLE\Computer Know-How\JabRef\Issues\#8278 Writing XMP metadata to PDFs skips my linked pdf file. Improve error messages\test writing metadata to pdfs.bib is C:\Users\Thilo\AppData\Local\org.jabref\JabRef\0.5a
ANTLR Tool version 4.7.2 used for code generation does not match the current runtime version 4.9.3
ANTLR Tool version 4.7.2 used for code generation does not match the current runtime version 4.9.3
[WARN] PDDocument - You are overwriting an existing file, this will produce a corrupted file if you're also read[WARN] PDDocument - You are overwriting an existing file, this will produce a corrupted file if you're also read[WARN] PDDocument - You are overwriting an existing file, this will produce a corrupted file if you're also read2022-04-11 18:33:37 [pool-2-thread-3] org.jabref.gui.JabRefDialogService.notify()
INFO: Success! Finished writing metadata.

Edit 2: Can still trigger this error with newest version of pull request:

com.google.common.util.concurrent.UncheckedExecutionException: java.lang.IllegalStateException: 1-based index not found: 11
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2055)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache.get(LocalCache.java:3966)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3989)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4950)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$LocalLoadingCache.getUnchecked(LocalCache.java:4956)
	at org.jabref@100.0.0/org.jabref.logic.pdf.FileAnnotationCache.getFromCache(FileAnnotationCache.java:52)
	at org.jabref@100.0.0/org.jabref.gui.entryeditor.fileannotationtab.FileAnnotationTabViewModel.lambda$reloadAnnotations$1(FileAnnotationTabViewModel.java:104)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
	at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
	at javafx.graphics/com.sun.glass.ui.win.WinApplication._enterNestedEventLoopImpl(Native Method)
	at javafx.graphics/com.sun.glass.ui.win.WinApplication._enterNestedEventLoop(WinApplication.java:211)
	at javafx.graphics/com.sun.glass.ui.Application.enterNestedEventLoop(Application.java:515)
	at javafx.graphics/com.sun.glass.ui.EventLoop.enter(EventLoop.java:107)
	at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(QuantumToolkit.java:631)
	at javafx.graphics/javafx.stage.Stage.showAndWait(Stage.java:469)
	at javafx.controls/javafx.scene.control.HeavyweightDialog.showAndWait(HeavyweightDialog.java:162)
	at javafx.controls/javafx.scene.control.Dialog.showAndWait(Dialog.java:346)
	at org.jabref@100.0.0/org.jabref.gui.JabRefDialogService.showErrorDialogAndWait(JabRefDialogService.java:192)
	at org.jabref@100.0.0/org.jabref.gui.FallbackExceptionHandler.lambda$uncaughtException$0(FallbackExceptionHandler.java:26)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:457)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:399)
	at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:456)
	at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
	at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
	at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184)
	at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.IllegalStateException: 1-based index not found: 11
	at pdfbox@3.0.0-RC1/org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:316)
	at pdfbox@3.0.0-RC1/org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:297)
	at pdfbox@3.0.0-RC1/org.apache.pdfbox.pdmodel.PDPageTree.get(PDPageTree.java:243)
	at org.jabref@100.0.0/org.jabref.logic.pdf.PdfAnnotationImporter.importAnnotations(PdfAnnotationImporter.java:49)
	at org.jabref@100.0.0/org.jabref.logic.pdf.EntryAnnotationImporter.lambda$importAnnotationsFromFiles$2(EntryAnnotationImporter.java:53)
	at java.base/java.util.Optional.ifPresent(Optional.java:178)
	at org.jabref@100.0.0/org.jabref.logic.pdf.EntryAnnotationImporter.importAnnotationsFromFiles(EntryAnnotationImporter.java:53)
	at org.jabref@100.0.0/org.jabref.logic.pdf.FileAnnotationCache$1.load(FileAnnotationCache.java:39)
	at org.jabref@100.0.0/org.jabref.logic.pdf.FileAnnotationCache$1.load(FileAnnotationCache.java:36)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3533)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2282)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2159)
	at com.google.common@31.1-jre/com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2049)
	... 27 more

Siedlerchr · 2022-04-11T16:50:32Z

Works without errors for me.

koppor · 2022-04-11T18:13:34Z

Note to self: File Annotation Service worked better if temp file is written to

…les# * upstream/main: Add lucence backwards codec (#8667) Fix XMP write (#8658)

koppor added 11 commits April 10, 2022 23:13

Move out FileUtil code outside of try-catch-block

1d81097

Additonally: Rename file -> path

Refine comments

9896059

Add a href to JavaDoc

60bf43e

Refines JavaDoc comment

124b370

Try to add synchronized to throttle writing

f3bf55c

Correctly log exception

5402a64

Try another way for a writing-workaround

014fd4d

Remove empty line

10319bc

Port writing code to EmbeddedBifFilePdfExporter

093659d

Synchronize also at other method

8f0b5d8

Fix mode when writing XMP

0275926

Fix compile error

d01cf4d

Try to synchronize on class variable

f92e42f

koppor added 5 commits April 11, 2022 00:37

Test other logging

0043824

Fix typo

6b657a8

Try other bridge

b99bd4b

Try to get rid off apache commons logging

f96c9b7

Trying other exclude

8edf6ad

koppor marked this pull request as ready for review April 10, 2022 22:54

Siedlerchr added 3 commits April 11, 2022 17:14

remove log4j stuff to fix build

0dde122

fix dep version

3702e97

Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Apr 11, 2022

Siedlerchr and others added 2 commits April 11, 2022 19:11

change to read from orig and write to temp back then

1da1fe5

Fix typo

0a145ab

calixtus approved these changes Apr 11, 2022

View reviewed changes

calixtus merged commit 85dff5f into main Apr 11, 2022

calixtus deleted the fixXMP branch April 11, 2022 18:30

Siedlerchr added a commit that referenced this pull request Apr 11, 2022

Merge remote-tracking branch 'upstream/main' into adddeletemultiplefi…

5c2dad9

…les# * upstream/main: Add lucence backwards codec (#8667) Fix XMP write (#8658)

This was referenced Apr 12, 2022

Vast Memory Consumption on Ubuntu 20.04 #8416

Closed

Add option to delete XMP metadata #8681

Closed

Illegal state exception after switching into the "file annotations" tab #8669

Closed

koppor mentioned this pull request Apr 18, 2022

Write XMP Button should be disabled when action is in progress #8691

Closed

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