Damaging changes to PDF after highlighting text

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wendyerb
Posts: 3
Joined: Tue Aug 28, 2018 10:57 am

Damaging changes to PDF after highlighting text

Post by wendyerb » Wed Aug 29, 2018 9:10 am

I was highlighting a PDF in the preview window of Bookends. I then looked at another article and when I came back to the one I'd highlighted, I noticed that some of the highlighting was floating in a new area (i.e., not where I'd made the initial highlighting). This brought to my attention the fact that the right-hand side of the article was cut off. I often use the "automatically resize" feature to view the full page width of the PDF, so I used this and still the text was cut off. I then opened the PDF in Adobe, and discovered it was cut off here - Finder showed a "Date Modified" time stamp for the PDF file from a minute earlier. The PDF was not cut off when I was highlighting it, and I never opened the file in Adobe (only after I noticed this problem), so there's nothing I did that should have caused this permanent change to the source file. This has now happened several times, and since these changes render the PDF illegible, I have had to find these papers again, and add them anew to my library. Since I can't predict which files will be ruined by highlighting, I can no longer highlight or take notes on any of my references. This is a huge problem, as it's one of the main reasons I purchased this software (as a new migrant from Sente). VERY disappointingly, one of my most important ebooks was modified by Bookends, rendering the text in this book nearly illegible due to a strange font change that has messed up the text spacing and essentially removed every instance where the letters "i" and "f" are found together. I'm extremely frustrated with this issue, as it is ruining my valuable PDF's, some of which are not easily replaced, and negatively impacting my work flow.

On that note, I really prefer that the highlights that I make to files using Bookends are not saved in the source PDF. That feature makes it quite inconvenient for cases when I wish to share a paper with a colleague, but don't want to send them a copy that's all marked up with my highlights.

Can you please address these issues?

I submitted this report via email on the Support tab 2 days ago, and have yet to receive a response, so I appreciate your prompt attention to this rather big issue.

On a related note, two minor issues I've encountered:
1) When adding PDF's to my library, there is no preview of the PDF when the article metadata isn't automatically detected by Bookends. This is annoying, as I have to close this window, view the paper in the preview window to copy the article title, then use the Autofill from Internet tool (again, no preview of the PDF appears) and use this copied text to search.

2) It's happened a number of times that when adding new PDFs to my library, they are occasionally added to existing references - references that do not correspond to the paper I'm adding. This is super annoying, as I'm often adding papers in small batches (5-10 papers at a time), and sometimes 2 of these papers will both get attached to the same reference.

I'm attaching screenshots demonstrating these issues.

Thanks for your attention.
Attachments
Screen Shot 2018-08-29 at 2.06.06 PM.png
PDF formatting changes - cropping
Screen Shot 2018-08-29 at 2.06.06 PM.png (204.79 KiB) Viewed 824 times
Screen Shot 2018-08-29 at 2.04.18 PM.png
PDF formatting changes - font
Screen Shot 2018-08-29 at 2.04.18 PM.png (250.43 KiB) Viewed 824 times
Screen Shot 2018-08-29 at 2.02.42 PM.png
No preview when using "Autocomplete Paper"
Screen Shot 2018-08-29 at 2.02.42 PM.png (107.96 KiB) Viewed 824 times

Jon
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Re: Damaging changes to PDF after highlighting text

Post by Jon » Wed Aug 29, 2018 9:20 am

The forum software has stopped sending emails for some reason, so I never received one from you.

You don't say what OS you're using. Your last issue makes me think it's Sierra. Is that correct? If so, there are lots of PDFKit bugs in Sierra that affect Bookends. You *must* upgrade to High Sierra.

In addition, Bookends 13.x is 64 bit, which fixes an old problem where large PDFs are not rendered properly. If you're still using Bookends 12.x that might explain the failure of a PDF to be rendered in the Autocomplete Paper sheet that you report.

If you *are* using High Sierra and Bookends 13.x already and still have these problems, here are my replies:

----------------

I've never heard of this cropping issue before. If you can send me a PDF *before* an issue occurs and then tell me what to do to make the problem appear that would be helpful.

You mention an ebook -- Bookends won't open ebooks, much less edit them. Did you mean PDF?

Bookends saves annotations to the PDF, that's a major feature, not a bug. If you don't want those shared with colleagues you can choose to export the PDF without annotations (there's also a setting in preferences that tells Bookends to remove the annotations when emailing a PDF).

As for each issue you reported, please break them down into individual problems and email tech support directly (support@sonnysoftware.com) -- one email per issue, and send whatever files I'll need to reproduce the problem, with instructions on how to reproduce. Sending a file that is already altered will not help, I already believe you see these issues.

Jon
Sonny Software

wendyerb
Posts: 3
Joined: Tue Aug 28, 2018 10:57 am

Re: Damaging changes to PDF after highlighting text

Post by wendyerb » Thu Aug 30, 2018 6:52 am

Hi there,

Thanks for the reply.

I included the OS and hardware details in my email using the support link but here they are again:

OS X El Capitan Version 10.11.6
MacBook Pro (Retina, 13-inch, Early 2015)
Processor 3.1 GHz Intel Core i7
Bookends 13.1.3

-- I've never heard of this cropping issue before. If you can send me a PDF *before* an issue occurs and then tell me what to do to make the problem appear that would be helpful.

Sure. I can't attach the files here, so could you advise me to which email address I can send them - shall I use support@sonnysoftware.com mentioned below?

-- You mention an ebook -- Bookends won't open ebooks, much less edit them. Did you mean PDF?

It is a PDF of a book.

-- Bookends saves annotations to the PDF, that's a major feature, not a bug. If you don't want those shared with colleagues you can choose to export the PDF without annotations (there's also a setting in preferences that tells Bookends to remove the annotations when emailing a PDF).

OK, great. I noticed that the annotations were in the PDF when I opened with Acrobat, so worried this was a permanent change. Great to know I can export without annotation. Thanks for the information!

-- As for each issue you reported, please break them down into individual problems and email tech support directly (support@sonnysoftware.com) -- one email per issue, and send whatever files I'll need to reproduce the problem, with instructions on how to reproduce. Sending a file that is already altered will not help, I already believe you see these issues.

Will do. Thanks.

Jon
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Re: Damaging changes to PDF after highlighting text

Post by Jon » Thu Aug 30, 2018 8:48 am

I haven't received any emails from you yet. But when you send one, please attach any files you want me to see to the email (yes, support@sonnysoftware.com).

I strongly suggest that you upgrade to High Sierra. I can't promise it will make a difference for you, but I can tell you that El Capitan also has PDFKit problems (every version of macOS after Maverick did, but the ones that affect Bookends seem to have been fixed in High Sierra).

Jon
Sonny Software

P.S. I think the forum email issue has been resolved. But it's still better better to send things to me directly via your email client.

doclrb
Posts: 5
Joined: Fri Aug 10, 2018 3:52 pm

Re: Damaging changes to PDF after highlighting text

Post by doclrb » Tue Oct 02, 2018 4:23 pm

"On a related note, two minor issues I've encountered:
1) When adding PDF's to my library, there is no preview of the PDF when the article metadata isn't automatically detected by Bookends. This is annoying, as I have to close this window, view the paper in the preview window to copy the article title, then use the Autofill from Internet tool (again, no preview of the PDF appears) and use this copied text to search"

I am experiencing this exact issue in High Sierra. With other struggles, I initially believed that it was operator error. But apparently not. TY for posting this bug.

doclrb
doclrb
Les R. Becker, Ph.D., MS.MEdL, NRP, CHSE
lesrbecker2@gmail.com

Jon
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Re: Damaging changes to PDF after highlighting text

Post by Jon » Tue Oct 02, 2018 4:29 pm

The PDF view has nothing to do with Bookends having detected metadata. I can be due to bugs in Sierra, it also can be due to having the Adobe PDF Plugin installed

https://www.sonnysoftware.com/faq/faq.h ... ems_dis101

If it's not one of those, you should be contacting tech support with screen snaps of what you see as a problem and a PDF that illustrates it.

support@sonnysoftware.com

(the tech support form isn't working at the moment).

Jon
Sonny Software

wendyerb
Posts: 3
Joined: Tue Aug 28, 2018 10:57 am

Re: Damaging changes to PDF after highlighting text

Post by wendyerb » Tue Oct 02, 2018 7:12 pm

I'm still working on getting a full backup of my laptop (long story short, my time capsule suddenly failed so I had to buy a new drive and start over). As soon as I can upgrade to High Sierra, I will advise as to the status of these issues.

Thanks!
Wendy

dvb
Posts: 1
Joined: Thu Feb 07, 2019 11:18 am

Re: Damaging changes to PDF after highlighting text

Post by dvb » Thu Feb 07, 2019 11:24 am

I am wondering if Wendy or Jon would be willing to share what they found on the cropping issue. I am having the same issue—in my case, it appears to happen inconsistently, or at least infrequently enough where I would not know how to replicate the problem.

Thank you!

Jon
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Joined: Tue Jul 13, 2004 6:27 pm
Location: Bethesda, MD
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Re: Damaging changes to PDF after highlighting text

Post by Jon » Thu Feb 07, 2019 12:09 pm

I'm afraid I have nothing to add. Bookends uses Apple's PDFKit APIs. If there are bugs in the OS they'll need to be fixed by Apple.

Jon
Sonny Software

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