Writing XMP metadata to PDFs skips my linked pdf file. Improve error messages

[ThiloteE]

JabRef version

Latest development branch build (please note build date below)

Operating system

Windows

Details on version and operating system

Windows 10 21H1

Checked with the latest development build

• I made a backup of my libraries before testing the latest development version.
• I have tested the latest development version and the problem persists

Steps to reproduce the behaviour

JabRef 5.4--2021-11-15--9955a33
Windows 10 10.0 amd64
Java 16.0.2
JavaFX 17.0.1+1

Writing XMP metadata to pdf(s) skips my linked pdf file

How to reproduce:

1. Have a pdf file with linked XMP metadata

2. drag this file into Jabref (a entry emerges; Let's call it X)

3. Have another entry (let's call it Y) in another library that also links to this same file

4. Write metadata from Y to pdf via the following feature:
   

5. Try to write metadata from X to pdf via the F6 feature.

As soon as you use Writing XMP metadata to PDFs (F6) feature the following message pops up, even though my file is linked:

Appendix

...

Log File

Paste an excerpt of your log file here

[ThiloteE]

Minimal example with steps to reproduce:

1. Have a pdf.
2. Have an entry in Jabref
3. Attach the pdf file to the entry.
4. Write XMP metadata from entry to pdf file (F6).

File gets skipped, there is the pop-up Edit: and XMP metadata will definitely NOT be written. I verified via Foxitreader.

Edit: If one uses the following feature, XMP metadata will be written!, but there is no pop-up:

[ThiloteE]

Additional info:

• I verified the written metadata by dragging the manipulated pdf file into Jabref. The new entry that was thereby generated still contained old library data and the data that was supposed to be written was missing.

• I can open my pdfs from within Jabref, and linked the files via the search expression feature of Jabref. I use this search expression: **/.*[auth.etal:regex("\\."," & "):regex("\\& etal","et al.")].*[Organization].*[YEAR].*\\.[extension].

• the issue also happens, when i attach a file to an entry via right click on entry and attach file.

• the issue also happens, when i attach a file by editing the file path in the general tab of the entry editor by right clicking the file and using the edit function.

• Maybe relevant: https://discourse.jabref.org/t/write-to-xmp-feature-seems-to-work-only-with-relative-path/1714

• Jabref Documentation about XMP Metadata: https://docs.jabref.org/advanced/xmp

[ThiloteE]

Uuuuh XMP metadata actually WAS WRITTEN, but does not get imported into Jabref

1. This is what i pushed to the file:

@Article{Thompson20200330MCR,
  author       = {Thompson, {Mark R.}},
  date         = {2020-03-30},
  journaltitle = {Global Asia},
  title        = {Middle-Class Remorse: Re-embracing Liberal Democracy in the Philippines and Thailand},
  language     = {English},
  number       = {1},
  pages        = {60--64},
  url          = {https://scholars.cityu.edu.hk/en/publications/publication(484a64e7-5da0-4ea6-affc-0d3e9ffdc7d7).html},
  urldate      = {2021-11-13},
  volume       = {15},
  abstract     = {Democracy in both Thailand and the Philippines has been crippled by support given to anti-democratic forces by intellectuals who foolishly endorsed leaders who have done serious damage to the prospects for democratic governance in both countries. The middle classes that supported those views are now seized by remorse, and it remains to be seen whether a course correction in both countries is on the horizon, writes Mark R. Thompson.},
  file         = {:Thompson (2020-03-30) middle-class-remorse-re-embracing-liberal-democracy-in-the-philippines-and-thailand.pdf:PDF},
  publisher    = {East Asia Foundation},
}

2. With Foxitreader i can see that this is the metadata attached to the pdf-file:
   

3. But when i drag the pdf into Jabref THIS is the entry that will be generated:

@InProceedings{RemorseEtAl2021Fhc,
  author = {Middle-Class Remorse and Re-embracing Liberal and Democracy in the Philippines and Thailand and By Mark and R. Thompson},
  date   = {2021},
  title  = {Firefox https://www.globalasia.org/v15no1/cover/middle-class-remorse-re-emb},
  file   = {:E\:/server-t-150/FAU/3. Semester/AER Demokratische Transformation in Asien/00 Hausarbeit Buente 3/Thompson (2020-03-30) middle-class-remorse-re-embracing-liberal-democracy-in-the-philippines-and-thailand.pdf:PDF},
}

[ThiloteE]

@btut explained why the import leads to different metadata displayed than actually is attached via XMP (https://discourse.jabref.org/t/extract-information-from-pdf-import/2899):

Indeed, if Grobid is enabled the importer uses the following order to obtain metadata:

    Look for bibtex entry on first page of pdf
    Look for embedded bib file
    Grobid
    XMP metadata
    Attempt to find metadata on first page (not in bibtex format).

If you want to force an XMP import, you can go to file → import → either to current or new library and select XMP-annotated PDF (last in the drop-down list) in the bottom right corner.

So out of the three issues i identified in this thread, only one is still open and the other two are solved:

• Different XMP metadata is shown upon import of pdf than was written to pdf. Solution see above.
• Metadata is not written to pdf. Solved --> it can be written by using
  
• Writing XMP metadata to PDFs skips my linked pdf file when using the Writing XMP metadata to PDFs (F6) feature. Not solved.

[btut]

Hi, sorry I only saw this issue now after you tagged me in the forum. I'll look into that last point. Thanks for the detailed report!

[ThiloteE]

Hey i just tried the new development version with the fix.

It works! Thank you! 👍

Unfortunately it does not work for all linked files. Out of 55 entries it returned 11 with error.

Here one example:

@Online{FreedomHouse2019Fit,
  date         = {2019},
  title        = {Freedom in the World 2019},
  url          = {https://freedomhouse.org/report/freedom-world/2019/democracy-retreat},
  organization = {Freedom House},
  subtitle     = {Democracy in Retreat},
  urldate      = {2021-09-30},
  comment      = {This is the overview on the website about their booklet and research "Freedom in the world 2019"},
  file         = {:Freedomhouse/Brandt et al. (2019) Freedomhouse. Freedom in the world 2019.pdf:PDF},
}

The corresponding error message was:

FreedomHouse2019Fit
  Error while writing 'E:\server-t-150\FAU\3. Semester\AER Demokratische Transformation in Asien\00 Hausarbeit Buente 3\Freedomhouse\Brandt et al. (2019) Freedomhouse. Freedom in the world 2019.pdf':
    null

I then checked the metadata that was attached to the file via foxitreader:

Then, i used the other method to write metadata (the one you can find in the general tab). This time it wrote correctly and this emerged: