When saving: The libary has been modified by another program #4877

JoKalliauer · 2019-04-09T14:56:22Z

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 )

open .bib-file
press "ctrl" & "s"
Repeat step 2 till Bug appears.
The message "The library has been modified by another program" appears
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

The text was updated successfully, but these errors were encountered:

bernhard-kleine · 2019-04-09T16:39:35Z

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

wujastyk · 2019-04-23T20:55:24Z

Me too. :-(

wujastyk · 2019-05-11T15:06:11Z

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 · 2019-05-12T07:49:46Z

@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 · 2019-05-12T14:59:35Z

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 · 2019-06-11T10:34:40Z

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 · 2019-06-12T06:41:39Z

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

wujastyk · 2019-06-12T15:13:32Z

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 · 2019-06-13T04:34:33Z

@JoKalliauer here is a minimum working example:

% Encoding: UTF-8

@Article{,
}

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

gitcanzo · 2019-09-05T10:07:05Z

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 · 2019-09-05T10:48:58Z

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

gitcanzo · 2019-09-05T11:03:40Z

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

Both save actions and autosave are disabled. The issue persists

AEgit · 2019-09-08T12:08:19Z

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 · 2019-09-12T22:08:50Z

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 · 2019-10-20T19:59:34Z

Refs #5085

Krzmbrzl · 2019-10-27T13:17:17Z

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 · 2019-10-27T14:34:05Z

@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 · 2019-10-27T16:43:48Z

@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 · 2019-10-27T16:50:36Z

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 · 2019-10-27T16:53:01Z

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 · 2019-10-28T19:03:55Z

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 · 2019-10-28T19:20:26Z

@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 · 2019-10-28T23:05:26Z

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 · 2024-05-20T16:16:22Z

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 · 2024-05-21T11:36:27Z

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

wujastyk · 2024-05-22T02:45:04Z

@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 · 2024-05-27T12:35:13Z

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 · 2024-05-27T16:23:42Z

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

wujastyk · 2024-05-28T00:14:20Z

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 · 2024-06-03T19:26:08Z

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 · 2024-06-03T21:26:48Z

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 · 2024-06-03T21:27:37Z

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 · 2024-06-03T22:22:16Z

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 · 2024-06-04T19:14:29Z

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?

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

wujastyk · 2024-06-04T21:34:01Z

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 · 2024-06-05T00:17:11Z

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 · 2024-06-07T14:58:39Z

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 · 2024-06-07T15:23:23Z

You are using dropbox, right?

wujastyk · 2024-06-07T15:33:47Z

Yes

koppor · 2024-06-12T13:18:11Z

Also happens when assigning a paper to a group

koppor · 2024-06-14T22:47:51Z

~~@wujastyk could you try #11282?~~

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

wujastyk · 2024-06-16T01:41:12Z

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 · 2024-06-16T20:48:54Z

@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 · 2024-08-15T07:32:29Z

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.

start a new entry
type some data
wait a bit while doing something else
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

not saving immediately,
then reading the disk data and comparing with the in-memory data and
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".

tobiasdiez added the export / save label Apr 9, 2019

AEgit mentioned this issue Sep 8, 2019

Jabref reports inexistent changes #5257

Closed

1 task

AEgit mentioned this issue Sep 21, 2019

Exception error for any keystroke & "library has been modified" #5296

Open

tobiasdiez added this to the v5.0 milestone Sep 27, 2019

koppor self-assigned this Oct 20, 2019

koppor modified the milestones: 5.14, 5.13 Apr 8, 2024

koppor reopened this May 21, 2024

Siedlerchr modified the milestones: 5.13, 5.14 May 28, 2024

koppor mentioned this issue Jun 3, 2024

Improve code of BibDataBaseDiff #11355

Merged

6 tasks

koppor mentioned this issue Jun 14, 2024

Fix cursor jumping #11282

Merged

6 tasks

koppor closed this as completed in #11282 Jun 17, 2024

koppor reopened this Aug 15, 2024

When saving: The libary has been modified by another program #4877

When saving: The libary has been modified by another program #4877

Comments

JoKalliauer commented Apr 9, 2019 • edited Loading

bernhard-kleine commented Apr 9, 2019

wujastyk commented Apr 23, 2019

wujastyk commented May 11, 2019

JoKalliauer commented May 12, 2019

wujastyk commented May 12, 2019 via email

sfo commented Jun 11, 2019 • edited Loading

JoKalliauer commented Jun 12, 2019

wujastyk commented Jun 12, 2019 via email

sfo commented Jun 13, 2019

gitcanzo commented Sep 5, 2019 • edited Loading

Siedlerchr commented Sep 5, 2019

gitcanzo commented Sep 5, 2019

AEgit commented Sep 8, 2019

AEgit commented Sep 12, 2019

koppor commented Oct 20, 2019

Krzmbrzl commented Oct 27, 2019

koppor commented Oct 27, 2019

tobiasdiez commented Oct 27, 2019

Krzmbrzl commented Oct 27, 2019

tobiasdiez commented Oct 27, 2019

reox commented Oct 28, 2019

JoKalliauer commented Oct 28, 2019

koppor commented Oct 28, 2019

wujastyk commented May 20, 2024

koppor commented May 21, 2024

wujastyk commented May 22, 2024 • edited Loading

reox commented May 27, 2024

Siedlerchr commented May 27, 2024

wujastyk commented May 28, 2024

wujastyk commented Jun 3, 2024

koppor commented Jun 3, 2024

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Siedlerchr commented Jun 7, 2024

wujastyk commented Jun 7, 2024 via email

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