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jlegewie / zotfile

Zotero plugin to manage your attachments: automatically rename, move, and attach PDFs (or other files) to Zotero items, sync PDFs from your Zotero library to your (mobile) PDF reader (e.g. an iPad, Android tablet, etc.), and extract PDF annotations.
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Comments after first page breaks Extracting Annotations #489

Open bittnerma opened 4 years ago

bittnerma commented 4 years ago

Hey, I think I came across a bug.

I've tried exporting the annotations of this pdf, however, it hangs at ~10% without continuing. Weirdly, when I remove all the comments after the first page like this it works fine.

I get the following two messages in in Error script console:

[JavaScript Warning: "Expected ‘none’, URL, or filter function but found ‘alpha(’.  Error in parsing value for ‘filter’.  Declaration dropped." {file: "chrome://zotero/content/progressWindow.xul" line: 0}]
[JavaScript Error: "TypeError: annotations is undefined" {file: "chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js" line: 1278}]
canvasMakeAnnoDims@chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js:1278:23
CanvasGraphics_paintFormXObjectBegin@chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js:1838:7
CanvasGraphics_executeOperatorList@chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js:769:11
TilinPattern_createPatternCanvas@chrome://zotfile/content/pdfextract/pdfjs/src/display/pattern_helper.js:365:7
TilingPattern_getPattern@chrome://zotfile/content/pdfextract/pdfjs/src/display/pattern_helper.js:413:36
CanvasGraphics_fill@chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js:1079:25
CanvasGraphics_executeOperatorList@chrome://zotfile/content/pdfextract/pdfjs/src/display/canvas.js:769:11
InternalRenderTask__next@chrome://zotfile/content/pdfextract/pdfjs/src/display/api.js:1434:30

I'm on Windows 10 running Zotero 5.0.92 and ZotFile 5.0.16

qqobb commented 4 years ago

I could reproduce the issue and error messages for your first file, not_working.pdf, with the same specifications for the setup. I'm not sure about the underlying cause, but the issue might be related to the version of the PDF format. These files use PDF version 1.6. Currently, ZotFile only supports older PDF formats properly. See https://github.com/jlegewie/zotfile/issues/418 and here for some related general suggestions.

You could convert not_working.pdf from PDF-1.6 to the older PDF-1.4 format. I followed https://superuser.com/a/185404 to do the conversion with Ghostscript and could then extract all annotations. The first annotation (note) was extracted twice, though. In the Error Console, your first warning message remained, but the second error message was gone.

The Zotero developers are working on updating the PDF annotation extraction code that ZotFile uses, see https://github.com/zotero/zotero/issues/1018. Your files might be useful for testing, so if possible, keep sharing them.

bittnerma commented 4 years ago

It worked! Thank you!

I've used Adobe Acrobat to convert to PDF-1.4 and now I can extract all annotations. I didn't have the problem that my first note was extracted twice, however, this might have something to do with the fact each of the highlights contains an annotation with the same text as the highlight.

The second error message was gone for me as well, but now it seems the first error message is repeated for each annotation.

Nevertheless, I'm happy that I'm able to get my annotations now. I'll keep the files up until the annotation extraction is updated.