[Skim-app-users] Reading Skim created PDF annotations cross platform?

[Hydro Meteor]

Hello all -

My colleagues and have a requirement to read-only PDFs that have been marked
up with annotations across multiple OS platforms for example Windows 7 or
perhaps Android (where the creating / editing of the annotations are done
with Skim on Mac OS X). We ran a few tests -- we took some PDF documents and
added annotations in Skim 1.3.14 (65). We then saved them as PDF bundles (
.pdfd ). We then zipped the PDF bundles on the Mac and moved them over to
Windows 7 and XP machines where we then unzipped the bundles. We then used
the latest version of Adobe Acrobat (Reader) to to read the corresponding
PDF contained within the bundle but Acrobat Reader complained and didn't
display the annotations. We also tried the the Windows PDF reader program
called SumatraPDF (version 1.6). Sumatra didn't complain but it also didn't
show any annotations. Any suggestions?

Thanks,

-Hydro

[Christiaan Hofman]

Post by Hydro Meteor
Hello all -
My colleagues and have a requirement to read-only PDFs that have been marked up with annotations across multiple OS platforms for example Windows 7 or perhaps Android (where the creating / editing of the annotations are done with Skim on Mac OS X). We ran a few tests -- we took some PDF documents and added annotations in Skim 1.3.14 (65). We then saved them as PDF bundles ( .pdfd ). We then zipped the PDF bundles on the Mac and moved them over to Windows 7 and XP machines where we then unzipped the bundles. We then used the latest version of Adobe Acrobat (Reader) to to read the corresponding PDF contained within the bundle but Acrobat Reader complained and didn't display the annotations. We also tried the the Windows PDF reader program called SumatraPDF (version 1.6). Sumatra didn't complain but it also didn't show any annotations. Any suggestions?
Thanks,
-Hydro

Have you read the FAQ on the Wiki? And why would Acrobat complain when you opened the PDF, it's just the normal original PDF (without the notes).

Christiaan

[Hydro Meteor]

Hi Christiaan,

Yes, my colleague and I have read the FAQ on the Wiki, it clearly states

The notes can even be viewed on Windows using the embedded .fdf file.

This is precisely why we chose to export the test PDF document (with
annotations) as a PDF bundle. We have not tried this with Adobe Acrobat
Reader X version 10.0.1 on a machine running Windows XP Pro and Windows 7
Home Edition (with the same PDF bundle unzipped to both NTFS and FAT
formatted volumes). The results are the same: when we open the FDF file from

The comments could not be imported because the document's permissions do

not allow comment import operations

I have screen captures of this that I'd be happy to share, and also a sample
PDF bundle (we have tried with a few different PDF documents to reduce the
odds that we somehow ended up with an anomaly).

Can you (or someone else in the community) please try this with Acrobat
Reader X 10.0.1? This is version of Reader is the most current version
available from Adobe when electing to download Acrobat from their web site
(I don't have any previous versions to test against).

Thanks,

-Hydro

Post by Hydro Meteor
Hello all -
My colleagues and have a requirement to read-only PDFs that have been

marked up with annotations across multiple OS platforms for example Windows
7 or perhaps Android (where the creating / editing of the annotations are
done with Skim on Mac OS X). We ran a few tests -- we took some PDF
documents and added annotations in Skim 1.3.14 (65). We then saved them as
PDF bundles ( .pdfd ). We then zipped the PDF bundles on the Mac and moved
them over to Windows 7 and XP machines where we then unzipped the bundles.
We then used the latest version of Adobe Acrobat (Reader) to to read the
corresponding PDF contained within the bundle but Acrobat Reader complained
and didn't display the annotations. We also tried the the Windows PDF reader
program called SumatraPDF (version 1.6). Sumatra didn't complain but it also
didn't show any annotations. Any suggestions?

Post by Hydro Meteor
Thanks,
-Hydro

Have you read the FAQ on the Wiki? And why would Acrobat complain when you
opened the PDF, it's just the normal original PDF (without the notes).
Christiaan
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[Christiaan Hofman]

Post by Hydro Meteor
Hi Christiaan,
Yes, my colleague and I have read the FAQ on the Wiki, it clearly states

The notes can even be viewed on Windows using the embedded .fdf file.
The comments could not be imported because the document's permissions do not allow comment import operations

I have screen captures of this that I'd be happy to share, and also a sample PDF bundle (we have tried with a few different PDF documents to reduce the odds that we somehow ended up with an anomaly).
Can you (or someone else in the community) please try this with Acrobat Reader X 10.0.1? This is version of Reader is the most current version available from Adobe when electing to download Acrobat from their web site (I don't have any previous versions to test against).
Thanks,
-Hydro

I can confirm that Acrobat Reader does this in the latest version(s) 10.0.3. This must be a problem from them, as there should be no permission problem with the PDF I tested (there wasn't any permission restriction set whatsoever, the message is lying). So they must just blankly refuse reading FDF files with Acrobat Reader, I think they want to sell more Acrobat Pro. We cannot help that. This means that your only options are using Acrobat Pro or saving with embedded notes (File > Export.., or using the skimpdf tool).

Christiaan

Post by Hydro Meteor

Hello all -
My colleagues and have a requirement to read-only PDFs that have been marked up with annotations across multiple OS platforms for example Windows 7 or perhaps Android (where the creating / editing of the annotations are done with Skim on Mac OS X). We ran a few tests -- we took some PDF documents and added annotations in Skim 1.3.14 (65). We then saved them as PDF bundles ( .pdfd ). We then zipped the PDF bundles on the Mac and moved them over to Windows 7 and XP machines where we then unzipped the bundles. We then used the latest version of Adobe Acrobat (Reader) to to read the corresponding PDF contained within the bundle but Acrobat Reader complained and didn't display the annotations. We also tried the the Windows PDF reader program called SumatraPDF (version 1.6). Sumatra didn't complain but it also didn't show any annotations. Any suggestions?
Thanks,
-Hydro

Have you read the FAQ on the Wiki? And why would Acrobat complain when you opened the PDF, it's just the normal original PDF (without the notes).
Christiaan
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[Maxwell, Adam R]

Post by Christiaan Hofman

Post by Hydro Meteor

The comments could not be imported because the document's permissions do not allow comment import operations

I have screen captures of this that I'd be happy to share, and also a sample PDF bundle (we have tried with a few different PDF documents to reduce the odds that we somehow ended up with an anomaly).
Can you (or someone else in the community) please try this with Acrobat Reader X 10.0.1? This is version of Reader is the most current version available from Adobe when electing to download Acrobat from their web site (I don't have any previous versions to test against).
Thanks,
-Hydro

I can confirm that Acrobat Reader does this in the latest version(s) 10.0.3. This must be a problem from them, as there should be no permission problem with the PDF I tested (there wasn't any permission restriction set whatsoever, the message is lying).

Can you enable user rights on the PDF?

http://help.adobe.com/en_US/Acrobat/8.0/Professional/help.html?content=WS58a04a822e3e50102bd615109794195ff-7e0d.html

Linked to from these sites:

http://acrobatusers.com/forum/collaboration-commenting/cannot-see-pdf-comments

http://stackoverflow.com/questions/635996/how-to-add-dynamically-add-comments-to-a-pdf-using-xfdf

ISTR from discussion on c.t.t that this is a problem with pdftex-produced PDFs, as noted here:

http://stackoverflow.com/questions/27482/latex-pdf-rights-management

[Christiaan Hofman]

Post by Maxwell, Adam R

Post by Christiaan Hofman

Post by Hydro Meteor

The comments could not be imported because the document's permissions do not allow comment import operations

I have screen captures of this that I'd be happy to share, and also a sample PDF bundle (we have tried with a few different PDF documents to reduce the odds that we somehow ended up with an anomaly).
Can you (or someone else in the community) please try this with Acrobat Reader X 10.0.1? This is version of Reader is the most current version available from Adobe when electing to download Acrobat from their web site (I don't have any previous versions to test against).
Thanks,
-Hydro

I can confirm that Acrobat Reader does this in the latest version(s) 10.0.3. This must be a problem from them, as there should be no permission problem with the PDF I tested (there wasn't any permission restriction set whatsoever, the message is lying).

Can you enable user rights on the PDF?

No, I don't have Pro.

Post by Maxwell, Adam R
http://help.adobe.com/en_US/Acrobat/8.0/Professional/help.html?content=WS58a04a822e3e50102bd615109794195ff-7e0d.html
http://acrobatusers.com/forum/collaboration-commenting/cannot-see-pdf-comments
http://stackoverflow.com/questions/635996/how-to-add-dynamically-add-comments-to-a-pdf-using-xfdf
http://stackoverflow.com/questions/27482/latex-pdf-rights-management

Apparently then it's what I thought: Adobe doesn't allow you to use Reader to add these annotations (unless somehow you use Pro to allow it). This seems to contradict the specs, which basically say that you encrypt to *restrict* what you can do, and the specs also don't seem to say anything about this particular right. That's the problem with working with a format owned by a commercial company.

Christiaan

[Hydro Meteor]

On Wed, Jun 8, 2011 at 3:41 PM, Christiaan Hofman <***@gmail.com>wrote:

[SNIP]

Post by Christiaan Hofman
Apparently then it's what I thought: Adobe doesn't allow you to use Reader
to add these annotations (unless somehow you use Pro to allow it). This
seems to contradict the specs, which basically say that you encrypt to
*restrict* what you can do, and the specs also don't seem to say anything
about this particular right. That's the problem with working with a format
owned by a commercial company.

We should take this to one of the standards organizations for violation of
ISO standards. How to do this? We could also possibly get the assistance of
the Electronic Frontier Foundation (EFF) -- for example, they could make a
phone call to Adobe or post something on their web site < http://www.eff.org>

-Hydro

Post by Christiaan Hofman
Christiaan
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[Hydro Meteor]

On Wed, Jun 8, 2011 at 3:41 PM, Christiaan Hofman <***@gmail.com>wrote:

[SNIP]

Apparently then it's what I thought: Adobe doesn't allow you to use Reader

Post by Christiaan Hofman
to add these annotations (unless somehow you use Pro to allow it). This
seems to contradict the specs, which basically say that you encrypt to
*restrict* what you can do, and the specs also don't seem to say anything
about this particular right. That's the problem with working with a format
owned by a commercial company.

In the vein of this thread, I took a PDF document which had no comments,
opened it with Preview Version 5.0.3 (504.1) on Mac OS X 10.6.7 and then I
added various annotations with Preview. I then saved the PDF and brought it
over to the very same Windows machine running Adobe Acrobat Reader (version
10.0.1) that I used a few days ago to try and read annotations egressed as a
PDF bundle from Skim. Very interestingly, Acrobat did not once complain
about reading the PDF with annotations saved from Preview and what is more,
I could read all of those annotations. So is Apple colluding with Adobe?
btw, I disagree with the comment that PDF is "a format owned by a commercial
company" per the following excerpt:

http://en.wikipedia.org/wiki/Pdf

Originally a proprietary
format<http://en.wikipedia.org/wiki/Proprietary_format>,

Post by Christiaan Hofman
PDF was officially released as an open standard<http://en.wikipedia.org/wiki/Open_standard>on July 1, 2008, and published by the International
Organization for Standardization<http://en.wikipedia.org/wiki/International_Organization_for_Standardization>as ISO
32000-1 <http://en.wikipedia.org/wiki/ISO_32000-1>:2008.

The Acrobat Reader is proprietary and yes is owned by a commercial company
(Adobe) but a variant of the originally proprietary format has been made
into an ISO standard. Is there not any interest in the Skim community to
pressure Adobe to "fix" Acrobat 10.x on Windows such that it will correctly
read annotations exported to PDF bundles by Skim?

-Hydro

Post by Christiaan Hofman
Christiaan

[Christiaan Hofman]

Post by Hydro Meteor
[SNIP]
Apparently then it's what I thought: Adobe doesn't allow you to use Reader to add these annotations (unless somehow you use Pro to allow it). This seems to contradict the specs, which basically say that you encrypt to *restrict* what you can do, and the specs also don't seem to say anything about this particular right. That's the problem with working with a format owned by a commercial company.
In the vein of this thread, I took a PDF document which had no comments, opened it with Preview Version 5.0.3 (504.1) on Mac OS X 10.6.7 and then I added various annotations with Preview. I then saved the PDF and brought it over to the very same Windows machine running Adobe Acrobat Reader (version 10.0.1) that I used a few days ago to try and read annotations egressed as a PDF bundle from Skim. Very interestingly, Acrobat did not once complain about reading the PDF with annotations saved from Preview and what is more, I could read all of those annotations.

Uhm, that's explained on the FAQ (and here). Again, those are different type of notes. We have many reasons to NOT save notes in the PDF as Preview does. Basically what Preview does is Skim's Export as PDF with Embedded Notes, which has its own problems (problems Preview also has, though you may not have noticed yet, for instance the fact that Apple does not support higher PDF versions.)

Post by Hydro Meteor
So is Apple colluding with Adobe?

No. You apparently don't understand the problem. These two things have nothing to do with each other. These are different types of notes in different places, so you should not compare them.

Post by Hydro Meteor
http://en.wikipedia.org/wiki/Pdf
Originally a proprietary format, PDF was officially released as an open standard on July 1, 2008, and published by the International Organization for Standardization as ISO 32000-1:2008.

No, it's adopted as an open standard, but it's developed and determined by Adobe. I shouldn't have used the word "owned", but it doesn't change the argument. They add stuff all the time, and the format does allow leeway of adding some hidden keys, as they apparently have done here, and note it's a key affecting only their products.

Post by Hydro Meteor
The Acrobat Reader is proprietary and yes is owned by a commercial company (Adobe) but a variant of the originally proprietary format has been made into an ISO standard. Is there not any interest in the Skim community to pressure Adobe to "fix" Acrobat 10.x on Windows such that it will correctly read annotations exported to PDF bundles by Skim?
-Hydro
Christiaan

You really think we can influence Adobe on this?

Christiaan

[Hydro Meteor]

Post by Hydro Meteor
Hi Christiaan,
Yes, my colleague and I have read the FAQ on the Wiki, it clearly states

The notes can even be viewed on Windows using the embedded .fdf file.

This is precisely why we chose to export the test PDF document (with
annotations) as a PDF bundle. We have not tried this with Adobe Acrobat
Reader X version 10.0.1 on a machine running Windows XP Pro and Windows 7
Home Edition (with the same PDF bundle unzipped to both NTFS and FAT
formatted volumes). The results are the same: when we open the FDF file from

The comments could not be imported because the document's permissions do

not allow comment import operations
I have screen captures of this that I'd be happy to share, and also a
sample PDF bundle (we have tried with a few different PDF documents to
reduce the odds that we somehow ended up with an anomaly).
Can you (or someone else in the community) please try this with Acrobat
Reader X 10.0.1? This is version of Reader is the most current version
available from Adobe when electing to download Acrobat from their web site
(I don't have any previous versions to test against).
Thanks,
-Hydro
I can confirm that Acrobat Reader does this in the latest version(s)
10.0.3. This must be a problem from them, as there should be no permission
problem with the PDF I tested (there wasn't any permission restriction set
whatsoever, the message is lying). So they must just blankly refuse reading
FDF files with Acrobat Reader, I think they want to sell more Acrobat Pro.
We cannot help that. This means that your only options are using Acrobat Pro
or saving with embedded notes (File > Export.., or using the skimpdf tool).

Thank you for confirming that its something new that has emerged and isn't
something I anamalous that I was possibly doing (glad to know I'm sane and
not seeing things) :-)

-Hydro

Post by Hydro Meteor
Christiaan

Post by Hydro Meteor
Hello all -
My colleagues and have a requirement to read-only PDFs that have been

marked up with annotations across multiple OS platforms for example Windows
7 or perhaps Android (where the creating / editing of the annotations are
done with Skim on Mac OS X). We ran a few tests -- we took some PDF
documents and added annotations in Skim 1.3.14 (65). We then saved them as
PDF bundles ( .pdfd ). We then zipped the PDF bundles on the Mac and moved
them over to Windows 7 and XP machines where we then unzipped the bundles.
We then used the latest version of Adobe Acrobat (Reader) to to read the
corresponding PDF contained within the bundle but Acrobat Reader complained
and didn't display the annotations. We also tried the the Windows PDF reader
program called SumatraPDF (version 1.6). Sumatra didn't complain but it also
didn't show any annotations. Any suggestions?

Post by Hydro Meteor
Thanks,
-Hydro

Have you read the FAQ on the Wiki? And why would Acrobat complain when you
opened the PDF, it's just the normal original PDF (without the notes).
Christiaan
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[Thomas Schneider]

Hydro:

I tried a similar thing with pdfd. The trouble is it's just a
directory that contains the original PDF along with markup files. I
found that actually embedding worked:

/Applications/Skim.app/Contents/SharedSupport/skimpdf embed $1

That (as part of a script where $1 represents the file name as an
argument) made a single file, which saves one the zipping.

Tom

Thomas D. Schneider, Ph.D.
National Institutes of Health
National Cancer Institute
Gene Regulation and Chromosome Biology Laboratory
Molecular Information Theory Group
Frederick, Maryland 21702-1201
***@mail.nih.gov
http://alum.mit.edu/www/toms (permanent)

[Hydro Meteor]

Hi Tom,

Thank you for the suggestion, but I'm a little bit unclear as to what
precisely I should substitute for $1 ? For example I tried this on a PDF

/Applications/Skim.app/Contents/SharedSupport/skimpdf embed xyz.pdfd
Cannot create PDF document
/Applications/Skim.app/Contents/SharedSupport/skimpdf
skimpdf embed IN_PDF_FILE [OUT_PDF_FILE]
skimpdf unembed IN_PDF_FILE [OUT_PDF_FILE]
skimpdf merge IN_PDF_FILE_1 IN_PDF_FILE_2 [OUT_PDF_FILE]
skimpdf extract IN_PDF_FILE [OUT_PDF_FILE] [-range START [LENGTH] | -page
PAGE1... | -odd | -even]
skimpdf help [VERB]
skimpdf version
SkimPDF command-line client, version 1.0

The input file is supposed to be a PDF not a PDF bundle. Most importantly,
we want to be able to read annotated notes from Skim on an OS other than Mac
OS X.

Thanks,

-Hydro

I tried a similar thing with pdfd. The trouble is it's just a
directory that contains the original PDF along with markup files. I
/Applications/Skim.app/Contents/SharedSupport/skimpdf embed $1
That (as part of a script where $1 represents the file name as an
argument) made a single file, which saves one the zipping.
Tom
Thomas D. Schneider, Ph.D.
National Institutes of Health
National Cancer Institute
Gene Regulation and Chromosome Biology Laboratory
Molecular Information Theory Group
Frederick, Maryland 21702-1201
http://alum.mit.edu/www/toms (permanent)
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[Thomas Schneider]

Post by Hydro Meteor
Thank you for the suggestion, but I'm a little bit unclear as to
what precisely I should substitute for $1 ? For example I tried this

The input pdf file ...

Post by Hydro Meteor

/Applications/Skim.app/Contents/SharedSupport/skimpdf embed xyz.pdfd
Cannot create PDF document
/Applications/Skim.app/Contents/SharedSupport/skimpdf

skimpdf embed IN_PDF_FILE [OUT_PDF_FILE]
skimpdf unembed IN_PDF_FILE [OUT_PDF_FILE]
skimpdf merge IN_PDF_FILE_1 IN_PDF_FILE_2 [OUT_PDF_FILE]
skimpdf extract IN_PDF_FILE [OUT_PDF_FILE] [-range START [LENGTH] | -page PAGE1... | -odd | -even]
skimpdf help [VERB]
skimpdf version
SkimPDF command-line client, version 1.0
The input file is supposed to be a PDF not a PDF bundle. Most
importantly, we want to be able to read annotated notes from Skim on
an OS other than Mac OS X.

I found that I could embed notes created by Skim on my Mac into a PDF
and then those notes display on Acrobat and survive transport to other
computers. That's perfect for me. I can use Skim as a tool to modify
notes, and I can move the resulting PDF to other systems.

The mechanism with 'skimnotes convert' essentially makes a directory
and the files in the directory contain the original (untouched) PDF
and the notes in plain text.

So you could use either or both mechanism depending on what you want
do do.

Tom

Thomas D. Schneider, Ph.D.
National Institutes of Health
National Cancer Institute
Gene Regulation and Chromosome Biology Laboratory
Molecular Information Theory Group
Frederick, Maryland 21702-1201
***@mail.nih.gov
http://alum.mit.edu/www/toms (permanent)