When saving: The libary has been modified by another program

[JoKalliauer]

Edit:
JabRef 5.0, 5.1, 5.2, 5.4 till current version (Nov2021) is affected.

If you add a comment please add

• your operating system
• encoding of the document (e.g. ASCII, ANSI, ISO-8859, UTF-16 , ...)
• the line-seperators used in the file (lineforward or cariage-return or both or mixed)
• the settings of Options > Preferences > File
  -- (a) Newline seperator (try LineForward)
  -- (b) Always reformat BIB file on save and export (try disabling)
  -- (c) Autosave local libraries (try disabling)

---

Original post

JabRef 5.0-dev--snapshot--2019-04-09--master--0dd091f31
Linux 4.15.0-47-generic amd64 
Java 1.8.0_201

Ubuntu 18.04

• I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

Steps to reproduce the behavior: (same as #4810 )

1. open .bib-file
2. press "ctrl" & "s"
3. Repeat step 2 till Bug appears.
4. The message "The library has been modified by another program" appears
5. DO NOT accept the changes, otherwise all entries will be doubled (click dismiss)
   
   

Log File

Opening: /home/jkalliau/Desktop/Jabrefissue/LargeFile.bib
Can only load style files: Preview
Vorschaustil geändert zu: Vorschau
Speichere Bibliothek...
Opening: /tmp/jabref2591679195168273738.bib
Opening: /home/jkalliau/Desktop/Jabrefissue/LargeFile.bib
Bibliothek gespeichert '/home/jkalliau/Desktop/Jabrefissue/LargeFile.bib'.

Terminal

16:45:54.405 [JavaFX Application Thread] INFO  org.jabref.logic.importer.OpenDatabase - Opening: /home/jkalliau/Desktop/Jabrefissue/LargeFile.bib
16:45:54.963 [JavaFX Application Thread] ERROR org.jabref.logic.citationstyle.CitationStyle - Can only load style files: Preview
16:45:55.220 [JavaFX Application Thread] INFO  org.jabref.gui.FXDialogService - Vorschaustil geändert zu: Vorschau
16:46:06.495 [JavaFX Application Thread] INFO  org.jabref.gui.FXDialogService - Speichere Bibliothek...
16:46:06.524 [pool-3-thread-2] INFO  org.jabref.logic.importer.OpenDatabase - Opening: /tmp/jabref2591679195168273738.bib
16:46:06.526 [pool-3-thread-2] INFO  org.jabref.logic.importer.OpenDatabase - Opening: /home/jkalliau/Desktop/Jabrefissue/LargeFile.bib
16:46:06.530 [JavaFX Application Thread] INFO  org.jabref.gui.FXDialogService - Bibliothek gespeichert '/home/jkalliau/Desktop/Jabrefissue/LargeFile.bib'.
16:53:39.039 [JavaFX Application Thread] INFO  org.jabref.gui.FXDialogService - In die Zwischenablage kopiert

[bernhard-kleine]

This is most interesting since you work with Linux. Obviously the error is indepent of the operation system.

[wujastyk]

Me too. :-(

[wujastyk]

Could this be something to do with Dropbox? I guess the Dropbox application (nemo-dropbox in Linux Mint) runs some kind of file-checking background task, and maybe JabRef is sensing that?

Is anyone who sees this "library modified" popup behaviour not run Dropbox?

[JoKalliauer]

@wujastyk : I storred it locally on the desktop, therefore it is not reletated to any sync-program.
Please also read @bernhard-kleine : comment: #4810 (comment)

[wujastyk]

I see. So it's not Dropbox. Thanks!

…

On Sun, 12 May 2019 at 01:49, Johannes Kalliauer ***@***.***> wrote: @wujastyk <https://github.com/wujastyk> : I storred it locally on the desktop, therefore it is not reletated to any sync-program. Please also read @bernhard-kleine <https://github.com/bernhard-kleine> : comment: #4810 (comment) <#4810 (comment)> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4877 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF2DBWFGGV2SY5NX2KCRB3PU7DZ7ANCNFSM4HES3FEQ> .

[sfo]

I can confirm this issue. It appears for files outside Dropbox, as well as for files within Dropbox and paused synchronization.

For me, it is independent from timing. I have the files on SSD. After editing, no matter how long, I save the file and the message appears.

---

JabRef 5.0-dev--snapshot--2019-06-10--master--eb42850f7
Linux 4.4.0-150-generic amd64
Java 1.8.0_212
Ubuntu 16.04

[JoKalliauer]

@sfo: How large is your libary? (filesize/entries)

[wujastyk]

Over 4000 Sent from Android phone

…

On Wed, 12 Jun 2019, 00:41 Johannes Kalliauer, ***@***.***> wrote: @sfo <https://github.com/sfo>: How large is your libary? (filesize/entries) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4877?email_source=notifications&email_token=AAF2DBXIPMGGK4K4XISPDO3P2CLCPA5CNFSM4HES3FE2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXPNDGI#issuecomment-501141913>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAF2DBUXPZFAO5457T7VPE3P2CLCPANCNFSM4HES3FEQ> .

[sfo]

@JoKalliauer here is a minimum working example:

% Encoding: UTF-8

@Article{,
}

@Comment{jabref-meta: databaseType:biblatex;}

[gitcanzo]

Same issue here (also using Jabref 5.0-dev). The message appears every time I save my library (even if no changes have been made). I do not have a big library, just about 100 entries. If I save the changes, all my entries are duplicated. My bib file is on a cloud folder (MEGA cloud, although that does not seem to be the issue). I am running Ubuntu Mate 19.04

[Siedlerchr]

Please check if you any save actions (library properties) or autosave enabled (preferences)

[gitcanzo]

Please check if you any save actions (library properties) or autosave enabled (preferences)

Both save actions and autosave are disabled. The issue persists

[AEgit]

JabRef 5.0-dev
Linux 5.0.0-27-generic amd64
Java 1.8.0_222

Can confirm this issue using the minimum example provided here (#4877 (comment)) by @sfo

"Save actions" are NOT enabled. "Autosave" is also NOT enabled.

Since the minimum example contains just one entry and I have stored the database on a fast M.2 SSD, this issue does not seem to be related to the size of the database or slow hardware.

[AEgit]

JabRef 5.0-dev
Linux 5.0.0-27-generic amd64
Java 11.0.4

Can confirm that this is still an issue with the current --edge snap version using Java 11 (I am just reporting this in case someone thought the switch to Java 11 had solved the problem). The minimum working example of @sfo (#4877 (comment)) is enough to be able to trigger this problematic behaviour.

[koppor]

Refs #5085

[Krzmbrzl]

JabRef 5.0.0-dev--2019-10-25----681d6aa6f
Linux 5.0.0-32-generic amd64 
Java 12.0.2

I can also confirm the bug. Happens every time to me though. If I can help by providing more information, just state what you'd need :)

[koppor]

@Krzmbrzl Thank you for the feedback and offer. I have a long-termin solution in my mind (see #5257 (comment)), but currently did not find the time to do it.

[tobiasdiez]

@Krzmbrzl you have coding experience, right? This bug is a bit hard to fix for us since non of the core developers can reproduce it. So it would be nice if you could try to debug it and find the origin of the problem (and in the best case also provide a solution).

[Krzmbrzl]

I do. However I am very busy atm and I'm afraid won't find the time necessary to do so properly... Plus I think I can't even set it up on my machine as I don't have JDK 12 available on my system

[tobiasdiez]

Sure, no problem. In case you find bit of time, you find everything that you need to setup the build locally here: https://github.com/JabRef/jabref/wiki/Guidelines-for-setting-up-a-local-workspace

[reox]

I have this issue too:

JabRef 5.0.0-dev--2019-10-25----b8d00f2bd
Linux 5.2.0-3-amd64 amd64 
Java 12.0.2

unfortunately I dont see any log output, as the debian package from the snapshots does not ship with log4j:

ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...

I suspected that maybe the noatime flag on my filesystem might causing this, but I verified on another filesystem with relatime that I get this message too.

[JoKalliauer]

@Krzmbrzl you have coding experience, right? This bug is a bit hard to fix for us since non of the core developers can reproduce it. So it would be nice if you could try to debug it and find the origin of the problem (and in the best case also provide a solution).

As a provisional workaround you can just add a button in the preferences to dissable the changes-feature.

[koppor]

Related:

00:03:19.723 [pool-9-thread-1] ERROR org.jabref.logic.autosaveandbackup.BackupManager - Error while saving to fileC:\TEMP\del.me.bib.sav
java.nio.file.FileSystemException: C:\TEMP\del.me.bib.sav -> C:\TEMP\del.me.bib.sav.bak: Der Prozess kann nicht auf die Datei zugreifen, da sie von einem anderen Prozess verwendet wird.

We should remove the sav and bak feature. This is so 2000. I forced to keep it in 2015, but I regret it now. Version control and backup feature are now common things.

Maybe, if we just remove bak and sav (and directly save to bib), all these change detection issues could be resolved.

[wujastyk]

JabRef 5.14--2024-05-20--18c3a55
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

This message is popping up all the time with the current test JR version (and versions for the last week or two). I've tried switching on and off the backup/autosave/autoreformat settings in different combinations, with no improvement. The message pops up multiple time even while editing a single entry. I have to hit "dismiss" to move on.

[koppor]

@wujastyk What is the result of "Review changes"?

[wujastyk]

@wujastyk What is the result of "Review changes"?

JabRef 5.14--2024-05-17--b12f65c
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

I started a new book entry. The message popped up, and I looked at "review changes":

As you see, the JabRef version has the citation key and the citationkey field.

Here's another:

[reox]

I saw this again several times now with

JabRef 5.13--2024-04-01--6bdcf63
Windows 11 10.0 amd64 
Java 21.0.2 
JavaFX 22+30

But I cannot even recognize anything that has changed:

Did I overlooked something or are these exactly the same contents?

[Siedlerchr]

This could be some whitespace/line ending stuff e..g \r\n vs \n

[wujastyk]

JabRef 5.14--2024-05-27--e1da33d
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

I'm sorry to shout, but this is driving me mad. I get this popup every time I edit an entry. When I choose "merge" to see what's going on, I frequently get something like this:

or - very often - no difference at all between the two merge columns.

It's not an issue of line-endings. All my files are thoroughly unix (and I've double checked).

[wujastyk]

JabRef 5.14--2024-06-03--67f74a3
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

Every time I save a new entry, I get the "modified by another program" popup. When I look at "merge" I see that it's always (almost always?) the field with the attached file that is causing the error message. I cannot see any difference in the field contents, but perhaps this is a clue to the issue?

[koppor]

Sorry to hear. It seems, we need a "trial and error" now. We are creating a debug version at #11355. -- The log of JabRef should show "Differences detected" if differences have been detected. Maybe, these can be used to check the cause. Could you please download the binary from there and report the output?

[koppor]

But I cannot even recognize anything that has changed:

@reox Could you please click on "Merge entries"? That dialog has a visual indicator what's changed. See screenshot of #4877 (comment).

[wujastyk]

I fetched 11355:
JabRef 5.14-PullRequest11355.166--2024-06-03--d97c29b
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

I didn't get the popup just adding a new entry without an attached file. But when I added the file, I got the popup.

And here's the log:

jabref.log

[Siedlerchr]

Thanks for the info. I put both into a test to see the visual differences and checked it with a hex editor, turns out it's an additional space before the word Contestation.
If you switch to "highlight characters" it will also highlight the position.

How did you add the file?

1. Automatic download?
2. Manual via + sign in general tab or Drag and drop?
3. What is your citation key pattern?

[wujastyk]

JabRef 5.14-PullRequest11355.166--2024-06-03--d97c29b
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

Now I have a situation where the popup happens every time I save, even when there are no changes at all, even when I'm not editing the entry that pops up.

jabref-2024-06-04_12.48.19.mp4

[wujastyk]

How did you add the file?

1. Automatic download?

2. Manual via + sign in general tab or Drag and drop?

3. What is your citation key pattern?

Great catch!

I added the file from my disk using the General tab and hitting the little + sign in the "file" field. Your no. 2 above. Not drag and drop.

My citation key pattern is [auth4:lower]-[year] (and I remove "-" from the "remove the following characters" group.

I have

[wujastyk]

JabRef 5.14--2024-05-29--6a63990
Linux 6.5.0-35-generic amd64
Java 21.0.2
JavaFX 22.0.1+7

This was an odd case. I deleted a short dummy entry "fo", and then got a popup saying that the library had been modified by another program. There was no attached PDF and the entry was very simple (a glossary entry for bib2gls). So it looked like I deleted the entry and then another program (?) added it again. I pressed "accept" and indeed the "fo" entry was back in the database. I deleted it a second time and then it stayed gone and there was no popup.

[Siedlerchr]

You are using dropbox, right?

[wujastyk]

Yes

[koppor]

Also happens when assigning a paper to a group

[koppor]

@wujastyk could you try #11282?

Update: Autosave does not yet work for the fix, so no need to try.

[wujastyk]

Oh, I already did. The old issue did not appear, but there was a new glitch. Adding a PDF and saving: the link to the PDF stopped working.

jabref02-2024-06-15_17.46.42.mp4

[koppor]

@wujastyk Thank you for testing! It were the two spaces in the file name. JabRef shrinks them to one; which is OK for text fields, but not for file paths 😅

I fixed it just now. Build should be available in 15 minutes.

[wujastyk]

JabRef 5.16--2024-08-13--70495a2
Linux 6.8.0-40-generic amd64
Java 21.0.2
JavaFX 22.0.2+4

"autosave local libraries" turned off.

1. start a new entry
2. type some data
3. wait a bit while doing something else
4. error message "the library has been modified by another program" pops up.

The merge screen shows that the "in jabref" data is ahead of the "on disk" data. And JabRef is

1. not saving immediately,
2. then reading the disk data and comparing with the in-memory data and
3. then throwing the warning.

I think that step 2 is premature. And JabRef thinks that the data I've typed since the last save is modification "by another program".