Add option to disable autolink files

[AEgit]

I am not sure whether this counts as a feature request or a bug.

JabRef 5.0-dev--snapshot--2019-07-06--master--add35be12
Windows 10 10.0 amd64
Java 1.8.0_211

In JabRef 3.8.2 it was possible to link previously downloaded PDFs to the database item using the "Get fulltext" button (see http://help.jabref.org/en/GetBibTeXDataFromDOI), if you had set a main file directory (http://help.jabref.org/en/FileLinks). In current development versions that does not appear to be possible anymore. Instead, JabRef apparently starts to automatically look for all files whose names start with the bibtex key (depending on your setting) and then allow you you add these files. I would prefer that this automatic behaviour was turned off (or if people like it, that there is at least a way of turning it off) and that the manual addition becomes possible again with a dedicated button.

If you have many supporting files the automatic behaviour auto file link behaviour can become a bit annoying, especially if you have Bibtex keys like the following "Berner2013" and "Berner2013_Test" (all the supporting files of "Berner2013_Test" will automatically show up for "Berner2013").

Furthermore, I have the impression that JabRef no longer checks just the main file directory (as it did in version 3.8.2) but seems to scan the whole file system? Can you confirm this? If that is the case, can you restore the old behaviour: I don't want to link PDFs that are not found in the dedicated PDF folder.

[Siedlerchr]

Hi,

you are right. Get fulltext only searches online, not local. This was on purpose. There is somewhere an issue about that.
You can however use Quality-> Automatically set file links for the selected entry.

The auto link behavior can be configured in the prefs -> File tab:
Autolink files that start with or exactly match the key or alternatively a RegEx.

However, there is currently no option to disable this feature for the entry editor,

Furthermore, I have the impression that JabRef no longer checks just the main file directory (as it did in version 3.8.2) but seems to scan the whole file system? Can you confirm this? If that is the case, can you restore the old behaviour: I don't want to link PDFs that are not found in the dedicated PDF folder.

JabRef checks the following directories:
// 1. library properties user-specific directory
// 2. library properties general directory
// 3. preferences directory
// 4. BIB file directory (if the option use as primary directory in the global prefs is checked, than this dir is searched first and takes precedence over all others)

I hope this helps to clarify the feature a bit.

[AEgit]

@Siedlerchr
Thank you for the explanation. Ok, so Quality -> Automatically set file links (or alternatively pressing "F7") will set the file links for the selected entry, is that correct? Or will it set the file links for ALL entries of the database?
If it is the former, I am ok with it: The functionality that "Get fulltext" originally provided has just been moved to another menu (I would say maybe less intuitive, but I reckon there are reasons) and it can even be used with a keyboard shortcut. If it is the latter, though, then the manual assignment of links for a SINGLE entry is still missing - I would really like to see that implemented in that case.

It would be nice, to disable the automatic autolink feature in the entry editor, since it can get quite confusing when you have lots of files, especially those that start with the same bibtex key.

Furthermore, the file row in the "General" tab of the entry editor should display more rows. Here an example of the same entry with JabRef 3.8.2 and JabRef 5.0:

JabRef 3.8.2

JabRef 5.0

As you can see, in the case of JabRef 5.0 only 3 rows are shown in the "File" part of the "General" tab. The rest can only be reached by scrolling down. In JabRef 3.8.2 all files are shown. Note, that in this case JabRef has been opened on a 40'' screen (4k) at max window height so this is definitely not an issue regarding the size of the monitor or its resolution. Rather, the standard settings for displaying things in the various entry editor tabs need some revamp (I think this applies to a couple of rows in the entry editor, but for now, this is the one I have spotted).

Thank you also very much for clarifying the way JabRef searches for linked files. Ok, in this case I will have to think about my current folder setup and where to store the JabRef database relative to the file folder.

[AEgit]

JabRef 5.3--2021-03-05--f7de0a6
Windows 10 10.0 amd64
Java 14.0.2
JavaFX 15.0.1+1

The issues and feature requests described in #5105 (comment) and #5105 (comment) still persist.

[ThiloteE]

Not relevant anymore:
I can confirm that automatically set file links (or alternatively pressing "F7") will set the file links for the selected entry(s).

Still relevant:
The file row in the "General" tab of the entry editor should display more rows indeed. Still relevant.

JabRef 5.4--2021-10-15--93b8025
Windows 10 10.0 amd64
Java 16.0.2
JavaFX 17.0.0.1+1

[ThiloteE]

Closing in favour of #8823 so that we don't have two issues for the same thing.

[claell]

@ThiloteE only the comment (#5105 (comment)) seems to be mentioning the same topic. The issue here is about something else. So I suggest reopening this 😃