Multiple notes not always exported

[rdiaz02]

Debug log ID

PBGVFXFM-refs-euc/6.7.263-7

What happened?

When items contain more than one note, not all notes are always exported. This (often) reproduces the problem: add a new note to one of the references, and export. The last note or notes added is (are) missing.

(If one adds a new item, it seems all of the notes are exported).

I am attaching the exported biblatex bib file (with a ".txt" added so I can upload it). Note that notes are missing in both items:

• In the first item, "a second note" is missing
• In the second item, "and note x5" is missing

test4.bib.txt

Edit: and as I continue playing with this, modifying notes (e.g., adding text to them) or even removing notes is not always reflected in the exported bibtex. Restarting zotero seems to solve the problem (so is this something with the cache? But this is an example where I am exporting manually, by clicking in the collection).

[retorquere]

According to PBGVFXFM-refs-euc/, your library looks like this:

a journalArticle with notes

• ""
• "a test note"
• "CITE PROJ 2024"
• "cited in Cornwallis and Griffin, 2024, with sentence ‚Äúwhether antibiotic tolerance evolves before resistance in cystic fibrosis infections‚Äù\n(p. 194)"

which is correctly exported in ghoul2023 (BBT skips empty notes)

a standalone note with content

• "cited in Cornwallis and Griffin, 2024, with sentence ‚Äúwhether antibiotic tolerance evolves before resistance in cystic fibrosis infections‚Äù\n(p. 194)"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "CITE PROJ 2024"

which is not exported; BBT does not export standalone notes

a journalArticle with notes

• ""
• "a third note nx3"
• "Note nx1"
• "Note nx2"
• "note x4"

which is correctly exported in yomismo2019b (BBT skips empty notes)

a standalone note with content

• "Note nx1"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "Note nx2"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "a third note nx3"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "note x4"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "a test note"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "a second test note"

which is not exported; BBT does not export standalone notes

a standalone note with content

• "and note x5"

which is not exported; BBT does not export standalone notes

[retorquere]

Edit: and as I continue playing with this, modifying notes (e.g., adding text to them) or even removing notes is not always reflected in the exported bibtex. Restarting zotero seems to solve the problem (so is this something with the cache? But this is an example where I am exporting manually, by clicking in the collection).

I need a debug log for when this happens.

[rdiaz02]

About previous report

Thanks, and apologies, because that is not what I intended to send. Specifically, I did not intend to send a library with standalone notes, and when I was looking at Zotero, in that library there were (as far as I recall) no standalone notes (though there could have been standalone notes in the Bin library), and the two items included notes, not present in the bib, but that do not seem to be in the library you received. Regardless, here are more debug logs and examples.

Reproducing the issue

I think often when I enable debugging and thus restart Zotero, the problem disappears. I am having difficulty reproducing the issue, but I just did.

This is the debug log id: FWQ5FFW7-refs-euc/6.7.263-7

This is what I see:

Zotero library:

The exported bib (which I am also attaching as a bib file)

test4_bib

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1
\par
n1\_4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {another\_note
\par
more notes
\par
n0\_0
\par
n2\_1
\par
n2\_2
\par
n2\_3},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4.z1.bib.txt

Issues:

• "n1_1 and more stuff over here\n\n and more content here" is missing from the item yomismo2019b (title = "Test of Notes")

• "another_note to which I add more content now" is missing from yomismo2019c (title = "Test of Notes, 2")

• And yomismo2019c has notes that are no longer there (they were removed to the Bin)

In this particular case, this issue was observed after Zotero was unresponsive (with CPU usage of 100%) for sometime. (This happens to me unpredictably from time to time, for no apparent reason ---current Zotero version is 7.0.11).

Reproducing the issue with logging enabled

Now, I restart Zotero with logging enabled. This is what I have in Zotero, same thing as before (this is a new screen capture, though):

z1-post

and this is the bib exported, again with notes missing (this is before generating the debug log --see below for debug log)

test4_bib_post

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1
\par
n1\_4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {another\_note
\par
more notes
\par
n0\_0
\par
n2\_1
\par
n2\_2
\par
n2\_3},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4-post-log-bib.txt

Now I generate the debug log:

Debug log ID: 4MZUIQGC-refs-euc/6.7.263-7

And here what I see after exporting after generating the debug log ID; same problems of missing notes and of notes that should not be there:

test4-post-log-post-debug-id-bib

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1
\par
n1\_4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {another\_note
\par
more notes
\par
n0\_0
\par
n2\_1
\par
n2\_2
\par
n2\_3},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4-post-log-post-debug-id.bib.txt

After emptying the Bin

Debug log ID: KLE2TR4Z-refs-euc/6.7.263-7

Same problems of missing notes and of notes that should not be there:

test4_bin_emptied

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1
\par
n1\_4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {another\_note
\par
more notes
\par
n0\_0
\par
n2\_1
\par
n2\_2
\par
n2\_3},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4_bin_emptied-bib.txt

Yes, I am aware images do not allow for debugging (they are here just to document what I see).

[rdiaz02]

Another two examples.

Two restarts later, and I add new text to item "test of notes, 2" (yomismo2019c)

Debug Log ID: 7L82GQBX-refs-euc/6.7.263-7

test4-post-rs


Notice the "and more to notes and more\n and some more" is missing:

test4-post-rs.bib

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1 and more stuff over here
\par
and more content here
\par
n1\_4
\par
more in n4 too},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {another\_note to which I add more content now
\par
more notes},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4-post-rs-bib.txt

I add more text to an existing note, but no newlines here

Debug Log ID: 7RRKSIJY-refs-euc/6.7.263-7

z1-post-rs

Notice how the note for item with title "test of notes" (yomismo2019b) is missing the "MORE" in note "n1_1 and more stuff over here MORE"

z1-post-rs.bib

@book{darwin2005,
  title = {On the {{Origin}} of {{Species}}},
  author = {Darwin, Charles},
  year = {2005},
  month = jun,
  url = {https://www.gutenberg.org/ebooks/8205},
  urldate = {2024-10-17},
  lccn = {EBook-No. 8205},
  keywords = {Evolution (Biology),Natural selection},
  note = {LoC Class QH: Science: Natural history},
  dateadded = {2024-10-17},
  datemodified = {2024-10-17T19:51:02Z},
  sortfield = {2024-10-17-19-51-00}
}

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {n1\_1 and more stuff over here
\par
and more content here
\par
n1\_4
\par
more in n4 too},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

@article{yomismo2019c,
  title = {Test of Notes, 2},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  year = {2019},
  journal = {from 2019 paper},
  volume = {15},
  number = {8},
  pages = {e1007246},
  urldate = {2020-10-18},
  note = {aaa I am the newest
\par
another\_note to which I add more content now
\par
more notes and more to notes and more
\par
and some more
\par
NEWEST},
  dateadded = {2024-12-23},
  datemodified = {2024-12-23T13:30:22Z},
  sortfield = {2024-12-23-13-30-02}
}

test4-post-rs-2-bib.txt

[retorquere]

I think often when I enable debugging and thus restart Zotero, the problem disappears. I am having difficulty reproducing the issue, but I just did.

I need to reword that if I wrote it down like that -- this is how it used to be for Zotero 6, but for 7, just enabling it is enough for most problems, and for startup problems, enabling it and disable - enable BBT is enough.

The exported bib (which I am also attaching as a bib file)

but in the first sample you uploaded as test4.bib.txt, you have

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  date = {2019},
  journaltitle = {from 2019 paper},
  shortjournal = {some journal},
  volume = {15},
  number = {8},
  pages = {e1007246},
  note = {a third note nx3
\par
Note nx1
\par
Note nx2
\par
note x4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

Yes, I am aware images do not allow for debugging (they are here just to document what I see).

I'd prefer it if you pasted the bibtex samples in, surrounded with

```
```

which is a little more compact, and it's searchable.

[rdiaz02]

I need to reword that if I wrote it down like that -- this is how it used to be for Zotero 6, but for 7, just enabling it is enough for most problems, and for startup problems, enabling it and disable - enable BBT is enough.

All the five new reports from today (2024-12-23) except for the first, have logging enabled.

but in the first sample you uploaded as test4.bib.txt, you have

@article{yomismo2019b,
  title = {Test of Notes},
  shorttitle = {A Test Entry},
  author = {{yomismo}, yo},
  date = {2019},
  journaltitle = {from 2019 paper},
  shortjournal = {some journal},
  volume = {15},
  number = {8},
  pages = {e1007246},
  note = {a third note nx3
\par
Note nx1
\par
Note nx2
\par
note x4},
  dateadded = {2024-12-20},
  datemodified = {2024-12-20T20:09:20Z},
  sortfield = {2024-12-20-20-02-23}
}

I am not sure I follow. All the bib files sent today have been generated today (all have Darwin's Origin of Species as one of the references). (Yes, it was a mistake on my part not to change the name of the library and the export. Sorry).

Yes, I am aware images do not allow for debugging (they are here just to document what I see).

I'd prefer it if you pasted the bibtex samples in, surrounded with

which is a little more compact, and it's searchable.

I just did, for the five cases I've reported today (in the original reports, though, I had also added the bib files, in addition to the images, with a ".txt" appended at end).