Zotfile does not extract annotations sometimes

KaiNLee

I have a PDF with extensive annotations. The tool in Zotero (Zotfile) that extracts annotations does not work with this file, but it does work with other ones. Advice? I'm happy to attach the file.

adamsmith

All annotated with the same software using the same type of annotations? (e.g. ZotFile doesn't support text boxes and doesn't support Skim annotations)

KaiNLee

Yes. Annotation consists of highlighting and comment bubbles inserted by PDFpenPro v 8.3.3, on an academic article from PLoSOne. A companion article (same first author) from PNAS extracts annotations just fine. Happy to send you both but can't see how to post my PDFs.

KaiNLee

What do you know? Came back after ~2 h and the extraction worked; even added on to the Notes file I'd started in frustration. Would be good to add a progress bar into Zotfile tool in future

KaiNLee

Ooops. Did not extract; it was the other file that I'd worked on that extracted. Apologies. Issue is still open.

Gurdas_Sandhu

So, the problem is with only one file? Do other files from PLoSOne work fine?

You can upload the two files to an online storage and post the link here.

KaiNLee

OK. There is a copy here, that I believe you can access:

https://www.dropbox.com/preview/ProblemFile-KaiLee copy.PDF?role=personal

adamsmith

no, that's not accessible (also doesn't look like a DB share link, which typically has a random string in it)

KaiNLee

OK, thanks. I'm not a frequent Dropbox user. Will see how to get you a working link.

KaiNLee

Try this: https://www.dropbox.com/s/4z3t6s3yctkdzvs/ProblemFile-KaiLee copy.PDF?dl=0

Apologies!

Gurdas_Sandhu

I was able to extract all highlighted and comment bubble annotations from that PDF.

While extracting, Zotfile shows a progress window in bottom-right, where under progress is marked by an incomplete circle.

Zotero 5.0.10 with Zotfile 5.0.4

KaiNLee

Thanks. What you report is what I expected. But when I right-click and select Extract Annotations, my Zotero does nothing at all. Advice?

Gurdas_Sandhu

I do not know if Zotero's Report ID and/or Debug ID capture issues related to add-ons, but those are additional options to help diagnose the issue.

https://www.zotero.org/support/reporting_problems

https://www.zotero.org/support/debug_output

KaiNLee

Here is the report I have submitted via Zotero Report ID: 2022098814

KaiNLee

The error (2022098814) is that for a specific file I am unable to extract annotations with Zotfile. No trouble found with other files.

The problem file is at https://www.dropbox.com/s/4z3t6s3yctkdzvs/ProblemFile-KaiLee copy.PDF?dl=0

Gurdas reports that s/he was able to extract annotations from this copy, however.

Advice?

KaiNLee

I also did a debug trace but unfortunately lost the case number. Below is the report.

PAC file installed from http://pac.stanford.edu/suproxy.pac

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{10fa933b-f7bb-c847-a7d3-a6049653c24c}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{10fa933b-f7bb-c847-a7d3-a6049653c24c}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{963f86b3-3689-b543-b74c-bbbfc1434efc}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{963f86b3-3689-b543-b74c-bbbfc1434efc}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{bdbde648-5a24-444d-89de-c9413aac1b4b}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{bdbde648-5a24-444d-89de-c9413aac1b4b}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

[JavaScript Error: "XML Parsing Error: not well-formed
Location: moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}
Line Number 1, Column 9:" {file: "moz-nullprincipal:{5d2436f7-6844-8340-9d70-2a89df5feaff}" line: 1 column: 9 source: "%PDF-1.3"}]

version => 4.0.29.22, platform => MacIntel, oscpu => Intel Mac OS X 10.12, locale => en-US, appName => Firefox, appVersion => 54.0.1

=========================================================

(5)(+0000000): SELECT indexedPages, totalPages AS total FROM fulltextItems WHERE itemID=?

(5)(+0000000): Binding parameter 1 of type int: 20640

(5)(+0001512): SELECT tagID FROM tags WHERE name=? AND type=? AND libraryID IS NULL

(5)(+0000000): Binding parameter 1 of type string: "_tablet"

(5)(+0000001): Binding parameter 2 of type int: 0

(5)(+0000000): SELECT tagID FROM tags WHERE name=? AND type=? AND libraryID IS NULL

(5)(+0000001): Binding parameter 1 of type string: "_tablet_modified"

(5)(+0000000): Binding parameter 2 of type int: 0

(5)(+0000001): SELECT COUNT(*) FROM itemTags WHERE itemID=? AND tagID IN ()

(5)(+0000000): Binding parameter 1 of type int: 20640

(5)(+0000003): SELECT indexedPages, totalPages AS total FROM fulltextItems WHERE itemID=?

(5)(+0000000): Binding parameter 1 of type int: 20640

(5)(+0001980): SELECT tagID FROM tags WHERE name=? AND type=? AND libraryID IS NULL

(5)(+0000000): Binding parameter 1 of type string: "_tablet"

(5)(+0000000): Binding parameter 2 of type int: 0

(5)(+0000001): SELECT tagID FROM tags WHERE name=? AND type=? AND libraryID IS NULL

(5)(+0000000): Binding parameter 1 of type string: "_tablet_modified"

(5)(+0000000): Binding parameter 2 of type int: 0

(5)(+0000001): SELECT COUNT(*) FROM itemTags WHERE itemID=? AND tagID IN ()

(5)(+0000000): Binding parameter 1 of type int: 20640

(5)(+0001318): SELECT IA.itemID FROM itemAttachments IA NATURAL JOIN items I LEFT JOIN itemData ID ON (IA.itemID=ID.itemID AND fieldID=1) LEFT JOIN itemDataValues IDV ON (ID.valueID=IDV.valueID) WHERE sourceItemID=? AND linkMode NOT IN (?) AND IA.itemID NOT IN (SELECT itemID FROM deletedItems) ORDER BY mimeType='application/pdf' DESC, value=? DESC, dateAdded ASC

(5)(+0000001): Binding parameter 1 of type int: 20639

(5)(+0000000): Binding parameter 2 of type int: 3

(5)(+0000000): Binding parameter 3 of type string: "https://doi.org/10.1371/journal.pone.0127533"