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* Error caused by document length
@ 2023-02-27 11:16 'Peter Vedal Utnes' via pandoc-discuss
       [not found] ` <7ed278f7-071b-4bcc-9f9a-e9dd5c09ee55n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 11:16 UTC (permalink / raw)
  To: pandoc-discuss


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We have a workflow in Open Journal Systems where we use Pandoc to convert 
word documents to EPUB, and then display them with an embedded EPUB app 
(Bibi). 

Our resulting EPUBs work fine with both debuggers and viewers like calibre. 
They work in Bibi, but only when they are reduced to a certain length. 
Whenever the files exceed approx 100 lines or 600 words, Bibi claims:

TypeError: Cannot read properties of undefined (reading ‘getAttribute’)

Meanwhile, the same documents works when converted to EPUB using other 
converters, or when I reduce the length (length, not size in bytes-- I've 
tried with graphics, still works). It suddenly works when I reduce the 
length by removing pure paragraph text, even though all the formatted 
elements (abstract, references, etc) are the same. 

I recognize that this problem is very specific to the interrelation pandoc 
<-> Bibi, but I'd be grateful for general troubleshooting suggestions. 

Thanks in advance, 

Peter

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* Re: Error caused by document length
       [not found] ` <7ed278f7-071b-4bcc-9f9a-e9dd5c09ee55n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 12:49   ` Bernardo C. D. A. Vasconcelos
       [not found]     ` <8f11cfaf-7c36-4cc6-9866-aa3741d965a4n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: Bernardo C. D. A. Vasconcelos @ 2023-02-27 12:49 UTC (permalink / raw)
  To: pandoc-discuss


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I do not know the answer to this problem in particular, but perhaps it is 
worth checking the main document *and* the bibliography for invisible 
control characters (e.g. `\X{A0}`). They tend to cause all sorts of strange 
problems that result in random error msgs.

On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:

> We have a workflow in Open Journal Systems where we use Pandoc to convert 
> word documents to EPUB, and then display them with an embedded EPUB app 
> (Bibi). 
>
> Our resulting EPUBs work fine with both debuggers and viewers like 
> calibre. They work in Bibi, but only when they are reduced to a certain 
> length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
> claims:
>
> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>
> Meanwhile, the same documents works when converted to EPUB using other 
> converters, or when I reduce the length (length, not size in bytes-- I've 
> tried with graphics, still works). It suddenly works when I reduce the 
> length by removing pure paragraph text, even though all the formatted 
> elements (abstract, references, etc) are the same. 
>
> I recognize that this problem is very specific to the interrelation pandoc 
> <-> Bibi, but I'd be grateful for general troubleshooting suggestions. 
>
> Thanks in advance, 
>
> Peter
>
>

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* Re: Error caused by document length
       [not found]     ` <8f11cfaf-7c36-4cc6-9866-aa3741d965a4n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 13:48       ` 'Peter Vedal Utnes' via pandoc-discuss
       [not found]         ` <4bd152b5-32f7-4f4c-9a9b-0d20afebea84n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 13:48 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 2542 bytes --]

I thank you for the suggestion. It is proving somewhat hard to 
(dis)confirm. I have made a testfile with just the word "test" pasted over 
and over again, with and without various formatting and with the same 
length or longer as the proper papers. This file consistently works. But 
when I attempt to do it with a regular research paper, it only works if I 
shorten it. Curiously, I can remove either half of the main text, or indeed 
sections here and there, randomly, and it works, but not with all of them 
present. I have combed it for special characters or tags, but cannot find 
any. 

mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. 
Vasconcelos:

> I do not know the answer to this problem in particular, but perhaps it is 
> worth checking the main document *and* the bibliography for invisible 
> control characters (e.g. `\X{A0}`). They tend to cause all sorts of strange 
> problems that result in random error msgs.
>
> On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
>
>> We have a workflow in Open Journal Systems where we use Pandoc to convert 
>> word documents to EPUB, and then display them with an embedded EPUB app 
>> (Bibi). 
>>
>> Our resulting EPUBs work fine with both debuggers and viewers like 
>> calibre. They work in Bibi, but only when they are reduced to a certain 
>> length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
>> claims:
>>
>> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>>
>> Meanwhile, the same documents works when converted to EPUB using other 
>> converters, or when I reduce the length (length, not size in bytes-- I've 
>> tried with graphics, still works). It suddenly works when I reduce the 
>> length by removing pure paragraph text, even though all the formatted 
>> elements (abstract, references, etc) are the same. 
>>
>> I recognize that this problem is very specific to the interrelation 
>> pandoc <-> Bibi, but I'd be grateful for general troubleshooting 
>> suggestions. 
>>
>> Thanks in advance, 
>>
>> Peter
>>
>>

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* Re: Error caused by document length
       [not found]         ` <4bd152b5-32f7-4f4c-9a9b-0d20afebea84n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 14:16           ` bernardovasconcelos-Re5JQEeQqe8AvxtiuMwx3w
       [not found]             ` <CAEJ71f529ORrJ+aaLU-8JFbE3uLvYkQdKcJjKSJb5mJSt+jOvA-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: bernardovasconcelos-Re5JQEeQqe8AvxtiuMwx3w @ 2023-02-27 14:16 UTC (permalink / raw)
  To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw

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Have you tried editing the original research paper in some minor way
(adding or removing a couple of characters) and then running it? This is a
completely wild guess, but maybe the text in the file is getting normalized
upon editing them, whereas the original research paper still contains the
unedited, unnormalized text.

On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <
pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:

> I thank you for the suggestion. It is proving somewhat hard to
> (dis)confirm. I have made a testfile with just the word "test" pasted over
> and over again, with and without various formatting and with the same
> length or longer as the proper papers. This file consistently works. But
> when I attempt to do it with a regular research paper, it only works if I
> shorten it. Curiously, I can remove either half of the main text, or indeed
> sections here and there, randomly, and it works, but not with all of them
> present. I have combed it for special characters or tags, but cannot find
> any.
>
> mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
> Vasconcelos:
>
>> I do not know the answer to this problem in particular, but perhaps it is
>> worth checking the main document *and* the bibliography for invisible
>> control characters (e.g. `\X{A0}`). They tend to cause all sorts of strange
>> problems that result in random error msgs.
>>
>> On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
>>
>>> We have a workflow in Open Journal Systems where we use Pandoc to
>>> convert word documents to EPUB, and then display them with an embedded EPUB
>>> app (Bibi).
>>>
>>> Our resulting EPUBs work fine with both debuggers and viewers like
>>> calibre. They work in Bibi, but only when they are reduced to a certain
>>> length. Whenever the files exceed approx 100 lines or 600 words, Bibi
>>> claims:
>>>
>>> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>>>
>>> Meanwhile, the same documents works when converted to EPUB using other
>>> converters, or when I reduce the length (length, not size in bytes-- I've
>>> tried with graphics, still works). It suddenly works when I reduce the
>>> length by removing pure paragraph text, even though all the formatted
>>> elements (abstract, references, etc) are the same.
>>>
>>> I recognize that this problem is very specific to the interrelation
>>> pandoc <-> Bibi, but I'd be grateful for general troubleshooting
>>> suggestions.
>>>
>>> Thanks in advance,
>>>
>>> Peter
>>>
>>> --
> You received this message because you are subscribed to a topic in the
> Google Groups "pandoc-discuss" group.
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> To unsubscribe from this group and all its topics, send an email to
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> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com
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> .
>

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* Re: Error caused by document length
       [not found]             ` <CAEJ71f529ORrJ+aaLU-8JFbE3uLvYkQdKcJjKSJb5mJSt+jOvA-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
@ 2023-02-27 14:23               ` 'Peter Vedal Utnes' via pandoc-discuss
       [not found]                 ` <db7972f9-8881-4941-92ea-9b8f51c0c404n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 14:23 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 4741 bytes --]

I am not sure what you mean by normalize in this context. I'll elaborate in 
case this is what you mean: In the interest of removing variables that 
might interfere with troubleshooting, I have copied the text from research 
papers (not just one, but a few), pasted it in notepad, copied and pasted 
it back into a new word-file (this is more thorough than "clear 
formatting"), ran this "pure" file through pandoc and I get the error. If I 
then randomly shorten the file, the error disappears. This is not the case 
for my "test" file, but only for research papers, which is baffling. I can 
only assume that pandoc responds to something like a character or in-text 
references in particular contexts, or as was my original hypothesis, the 
number of lines or columns in the EPUB. 

mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:

> Have you tried editing the original research paper in some minor way 
> (adding or removing a couple of characters) and then running it? This is a 
> completely wild guess, but maybe the text in the file is getting normalized 
> upon editing them, whereas the original research paper still contains the 
> unedited, unnormalized text.
>
> On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <
> pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>
>> I thank you for the suggestion. It is proving somewhat hard to 
>> (dis)confirm. I have made a testfile with just the word "test" pasted over 
>> and over again, with and without various formatting and with the same 
>> length or longer as the proper papers. This file consistently works. But 
>> when I attempt to do it with a regular research paper, it only works if I 
>> shorten it. Curiously, I can remove either half of the main text, or indeed 
>> sections here and there, randomly, and it works, but not with all of them 
>> present. I have combed it for special characters or tags, but cannot find 
>> any. 
>>
>> mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. 
>> Vasconcelos:
>>
>>> I do not know the answer to this problem in particular, but perhaps it 
>>> is worth checking the main document *and* the bibliography for 
>>> invisible control characters (e.g. `\X{A0}`). They tend to cause all sorts 
>>> of strange problems that result in random error msgs.
>>>
>>> On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
>>>
>>>> We have a workflow in Open Journal Systems where we use Pandoc to 
>>>> convert word documents to EPUB, and then display them with an embedded EPUB 
>>>> app (Bibi). 
>>>>
>>>> Our resulting EPUBs work fine with both debuggers and viewers like 
>>>> calibre. They work in Bibi, but only when they are reduced to a certain 
>>>> length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
>>>> claims:
>>>>
>>>> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>>>>
>>>> Meanwhile, the same documents works when converted to EPUB using other 
>>>> converters, or when I reduce the length (length, not size in bytes-- I've 
>>>> tried with graphics, still works). It suddenly works when I reduce the 
>>>> length by removing pure paragraph text, even though all the formatted 
>>>> elements (abstract, references, etc) are the same. 
>>>>
>>>> I recognize that this problem is very specific to the interrelation 
>>>> pandoc <-> Bibi, but I'd be grateful for general troubleshooting 
>>>> suggestions. 
>>>>
>>>> Thanks in advance, 
>>>>
>>>> Peter
>>>>
>>>> -- 
>> You received this message because you are subscribed to a topic in the 
>> Google Groups "pandoc-discuss" group.
>> To unsubscribe from this topic, visit 
>> https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to 
>> pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com 
>> <https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>

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* Re: Error caused by document length
       [not found]                 ` <db7972f9-8881-4941-92ea-9b8f51c0c404n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 14:33                   ` 'Peter Vedal Utnes' via pandoc-discuss
       [not found]                     ` <bc147d77-69c9-4e5d-82a6-e149f662a823n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 14:33 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 5400 bytes --]

I just did some further testing, and replaced the sections that I would 
otherwise have removed with as many words and paragraphs, but no signs, 
only "test test test" etc. The document then works. So I was wrong about 
the length: It must be some character or symbol producing the error (only 
with pandoc, not other EPUB converters). Any idea how to further isolate 
it, or how to circumvent with a pandoc command or template?

Thanks for the help so far, Bernardo.



mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:

> I am not sure what you mean by normalize in this context. I'll elaborate 
> in case this is what you mean: In the interest of removing variables that 
> might interfere with troubleshooting, I have copied the text from research 
> papers (not just one, but a few), pasted it in notepad, copied and pasted 
> it back into a new word-file (this is more thorough than "clear 
> formatting"), ran this "pure" file through pandoc and I get the error. If I 
> then randomly shorten the file, the error disappears. This is not the case 
> for my "test" file, but only for research papers, which is baffling. I can 
> only assume that pandoc responds to something like a character or in-text 
> references in particular contexts, or as was my original hypothesis, the 
> number of lines or columns in the EPUB. 
>
> mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
>
>> Have you tried editing the original research paper in some minor way 
>> (adding or removing a couple of characters) and then running it? This is a 
>> completely wild guess, but maybe the text in the file is getting normalized 
>> upon editing them, whereas the original research paper still contains the 
>> unedited, unnormalized text.
>>
>> On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <
>> pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>>
>>> I thank you for the suggestion. It is proving somewhat hard to 
>>> (dis)confirm. I have made a testfile with just the word "test" pasted over 
>>> and over again, with and without various formatting and with the same 
>>> length or longer as the proper papers. This file consistently works. But 
>>> when I attempt to do it with a regular research paper, it only works if I 
>>> shorten it. Curiously, I can remove either half of the main text, or indeed 
>>> sections here and there, randomly, and it works, but not with all of them 
>>> present. I have combed it for special characters or tags, but cannot find 
>>> any. 
>>>
>>> mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. 
>>> Vasconcelos:
>>>
>>>> I do not know the answer to this problem in particular, but perhaps it 
>>>> is worth checking the main document *and* the bibliography for 
>>>> invisible control characters (e.g. `\X{A0}`). They tend to cause all sorts 
>>>> of strange problems that result in random error msgs.
>>>>
>>>> On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes 
>>>> wrote:
>>>>
>>>>> We have a workflow in Open Journal Systems where we use Pandoc to 
>>>>> convert word documents to EPUB, and then display them with an embedded EPUB 
>>>>> app (Bibi). 
>>>>>
>>>>> Our resulting EPUBs work fine with both debuggers and viewers like 
>>>>> calibre. They work in Bibi, but only when they are reduced to a certain 
>>>>> length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
>>>>> claims:
>>>>>
>>>>> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>>>>>
>>>>> Meanwhile, the same documents works when converted to EPUB using other 
>>>>> converters, or when I reduce the length (length, not size in bytes-- I've 
>>>>> tried with graphics, still works). It suddenly works when I reduce the 
>>>>> length by removing pure paragraph text, even though all the formatted 
>>>>> elements (abstract, references, etc) are the same. 
>>>>>
>>>>> I recognize that this problem is very specific to the interrelation 
>>>>> pandoc <-> Bibi, but I'd be grateful for general troubleshooting 
>>>>> suggestions. 
>>>>>
>>>>> Thanks in advance, 
>>>>>
>>>>> Peter
>>>>>
>>>>> -- 
>>> You received this message because you are subscribed to a topic in the 
>>> Google Groups "pandoc-discuss" group.
>>> To unsubscribe from this topic, visit 
>>> https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe
>>> .
>>> To unsubscribe from this group and all its topics, send an email to 
>>> pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com 
>>> <https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>>

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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                     ` <bc147d77-69c9-4e5d-82a6-e149f662a823n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 14:54                       ` Bastien DUMONT
  2023-02-27 15:45                         ` Bernardo C. D. A. Vasconcelos
  2023-02-27 16:08                       ` John MacFarlane
  1 sibling, 1 reply; 14+ messages in thread
From: Bastien DUMONT @ 2023-02-27 14:54 UTC (permalink / raw)
  To: 'Peter Vedal Utnes' via pandoc-discuss

Maybe you could restore the paragraphs you replaced with "test" one by one and convert the document until Bidi throws an error. Then, you can remove the sentences of the offending paragraph one by one until the document is read again without error. Thus you could isolate at least one of the sentences that cause the error.

Le Monday 27 February 2023 à 06:33:28AM, 'Peter Vedal Utnes' via pandoc-discuss a écrit :
> I just did some further testing, and replaced the sections that I would
> otherwise have removed with as many words and paragraphs, but no signs, only
> "test test test" etc. The document then works. So I was wrong about the length:
> It must be some character or symbol producing the error (only with pandoc, not
> other EPUB converters). Any idea how to further isolate it, or how to
> circumvent with a pandoc command or template?
> 
> Thanks for the help so far, Bernardo.
> 
> 
> 
> mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
> 
>     I am not sure what you mean by normalize in this context. I'll elaborate in
>     case this is what you mean: In the interest of removing variables that
>     might interfere with troubleshooting, I have copied the text from research
>     papers (not just one, but a few), pasted it in notepad, copied and pasted
>     it back into a new word-file (this is more thorough than "clear
>     formatting"), ran this "pure" file through pandoc and I get the error. If I
>     then randomly shorten the file, the error disappears. This is not the case
>     for my "test" file, but only for research papers, which is baffling. I can
>     only assume that pandoc responds to something like a character or in-text
>     references in particular contexts, or as was my original hypothesis, the
>     number of lines or columns in the EPUB. 
> 
>     mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...@gmail.com:
> 
>         Have you tried editing the original research paper in some minor way
>         (adding or removing a couple of characters) and then running it? This
>         is a completely wild guess, but maybe the text in the file is getting
>         normalized upon editing them, whereas the original research paper still
>         contains the unedited, unnormalized text.
> 
>         On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss
>         <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> 
>             I thank you for the suggestion. It is proving somewhat hard to
>             (dis)confirm. I have made a testfile with just the word "test"
>             pasted over and over again, with and without various formatting and
>             with the same length or longer as the proper papers. This file
>             consistently works. But when I attempt to do it with a regular
>             research paper, it only works if I shorten it. Curiously, I can
>             remove either half of the main text, or indeed sections here and
>             there, randomly, and it works, but not with all of them present. I
>             have combed it for special characters or tags, but cannot find
>             any. 
> 
>             mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
>             Vasconcelos:
> 
>                 I do not know the answer to this problem in particular, but
>                 perhaps it is worth checking the main document and the
>                 bibliography for invisible control characters (e.g. `\X{A0}`).
>                 They tend to cause all sorts of strange problems that result in
>                 random error msgs.
> 
>                 On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal
>                 Utnes wrote:
> 
>                     We have a workflow in Open Journal Systems where we use
>                     Pandoc to convert word documents to EPUB, and then display
>                     them with an embedded EPUB app (Bibi). 
> 
>                     Our resulting EPUBs work fine with both debuggers and
>                     viewers like calibre. They work in Bibi, but only when they
>                     are reduced to a certain length. Whenever the files exceed
>                     approx 100 lines or 600 words, Bibi claims:
> 
>                     TypeError: Cannot read properties of undefined (reading
>                     ‘getAttribute’)
>                    
>                     Meanwhile, the same documents works when converted to EPUB
>                     using other converters, or when I reduce the length
>                     (length, not size in bytes-- I've tried with graphics,
>                     still works). It suddenly works when I reduce the length by
>                     removing pure paragraph text, even though all the formatted
>                     elements (abstract, references, etc) are the same. 
> 
>                     I recognize that this problem is very specific to the
>                     interrelation pandoc <-> Bibi, but I'd be grateful for
>                     general troubleshooting suggestions. 
> 
>                     Thanks in advance, 
> 
>                     Peter
> 
> 
>             --
>             You received this message because you are subscribed to a topic in
>             the Google Groups "pandoc-discuss" group.
>             To unsubscribe from this topic, visit [1]https://groups.google.com/
>             d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe.
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>             To view this discussion on the web visit [2]https://
>             groups.google.com/d/msgid/pandoc-discuss/
>             4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com.
> 
> --
> You received this message because you are subscribed to the Google Groups
> "pandoc-discuss" group.
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> to [3]pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
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> pandoc-discuss/bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com.
> 
> References:
> 
> [1] https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe
> [2] https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com?utm_medium=email&utm_source=footer
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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
  2023-02-27 14:54                       ` Bastien DUMONT
@ 2023-02-27 15:45                         ` Bernardo C. D. A. Vasconcelos
  0 siblings, 0 replies; 14+ messages in thread
From: Bernardo C. D. A. Vasconcelos @ 2023-02-27 15:45 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 6856 bytes --]

Also, maybe this could help: https://www.soscisurvey.de/tools/view-chars.php


On Monday, February 27, 2023 at 11:54:52 AM UTC-3 Bastien DUMONT wrote:

> Maybe you could restore the paragraphs you replaced with "test" one by one 
> and convert the document until Bidi throws an error. Then, you can remove 
> the sentences of the offending paragraph one by one until the document is 
> read again without error. Thus you could isolate at least one of the 
> sentences that cause the error.
>
> Le Monday 27 February 2023 à 06:33:28AM, 'Peter Vedal Utnes' via 
> pandoc-discuss a écrit :
> > I just did some further testing, and replaced the sections that I would
> > otherwise have removed with as many words and paragraphs, but no signs, 
> only
> > "test test test" etc. The document then works. So I was wrong about the 
> length:
> > It must be some character or symbol producing the error (only with 
> pandoc, not
> > other EPUB converters). Any idea how to further isolate it, or how to
> > circumvent with a pandoc command or template?
> > 
> > Thanks for the help so far, Bernardo.
> > 
> > 
> > 
> > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
> > 
> > I am not sure what you mean by normalize in this context. I'll elaborate 
> in
> > case this is what you mean: In the interest of removing variables that
> > might interfere with troubleshooting, I have copied the text from 
> research
> > papers (not just one, but a few), pasted it in notepad, copied and pasted
> > it back into a new word-file (this is more thorough than "clear
> > formatting"), ran this "pure" file through pandoc and I get the error. 
> If I
> > then randomly shorten the file, the error disappears. This is not the 
> case
> > for my "test" file, but only for research papers, which is baffling. I 
> can
> > only assume that pandoc responds to something like a character or in-text
> > references in particular contexts, or as was my original hypothesis, the
> > number of lines or columns in the EPUB. 
> > 
> > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
> > 
> > Have you tried editing the original research paper in some minor way
> > (adding or removing a couple of characters) and then running it? This
> > is a completely wild guess, but maybe the text in the file is getting
> > normalized upon editing them, whereas the original research paper still
> > contains the unedited, unnormalized text.
> > 
> > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss
> > <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> > 
> > I thank you for the suggestion. It is proving somewhat hard to
> > (dis)confirm. I have made a testfile with just the word "test"
> > pasted over and over again, with and without various formatting and
> > with the same length or longer as the proper papers. This file
> > consistently works. But when I attempt to do it with a regular
> > research paper, it only works if I shorten it. Curiously, I can
> > remove either half of the main text, or indeed sections here and
> > there, randomly, and it works, but not with all of them present. I
> > have combed it for special characters or tags, but cannot find
> > any. 
> > 
> > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
> > Vasconcelos:
> > 
> > I do not know the answer to this problem in particular, but
> > perhaps it is worth checking the main document and the
> > bibliography for invisible control characters (e.g. `\X{A0}`).
> > They tend to cause all sorts of strange problems that result in
> > random error msgs.
> > 
> > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal
> > Utnes wrote:
> > 
> > We have a workflow in Open Journal Systems where we use
> > Pandoc to convert word documents to EPUB, and then display
> > them with an embedded EPUB app (Bibi). 
> > 
> > Our resulting EPUBs work fine with both debuggers and
> > viewers like calibre. They work in Bibi, but only when they
> > are reduced to a certain length. Whenever the files exceed
> > approx 100 lines or 600 words, Bibi claims:
> > 
> > TypeError: Cannot read properties of undefined (reading
> > ‘getAttribute’)
> > 
> > Meanwhile, the same documents works when converted to EPUB
> > using other converters, or when I reduce the length
> > (length, not size in bytes-- I've tried with graphics,
> > still works). It suddenly works when I reduce the length by
> > removing pure paragraph text, even though all the formatted
> > elements (abstract, references, etc) are the same. 
> > 
> > I recognize that this problem is very specific to the
> > interrelation pandoc <-> Bibi, but I'd be grateful for
> > general troubleshooting suggestions. 
> > 
> > Thanks in advance, 
> > 
> > Peter
> > 
> > 
> > --
> > You received this message because you are subscribed to a topic in
> > the Google Groups "pandoc-discuss" group.
> > To unsubscribe from this topic, visit [1]https://groups.google.com/
> > d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe.
> > To unsubscribe from this group and all its topics, send an email to
> > pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> > To view this discussion on the web visit [2]https://
> > groups.google.com/d/msgid/pandoc-discuss/
> > 4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com.
> > 
> > --
> > You received this message because you are subscribed to the Google Groups
> > "pandoc-discuss" group.
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email
> > to [3]pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
> > To view this discussion on the web visit [4]
> https://groups.google.com/d/msgid/
> > pandoc-discuss/bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com.
> > 
> > References:
> > 
> > [1] 
> https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe
> > [2] 
> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com?utm_medium=email&utm_source=footer
> > [3] mailto:pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
> > [4] 
> https://groups.google.com/d/msgid/pandoc-discuss/bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com?utm_medium=email&utm_source=footer
>
>

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[-- Attachment #1.2: Type: text/html, Size: 11602 bytes --]

^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                     ` <bc147d77-69c9-4e5d-82a6-e149f662a823n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  2023-02-27 14:54                       ` Bastien DUMONT
@ 2023-02-27 16:08                       ` John MacFarlane
       [not found]                         ` <0AFB3E23-B7C1-49E8-9F8A-12716F6A2C40-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
  1 sibling, 1 reply; 14+ messages in thread
From: John MacFarlane @ 2023-02-27 16:08 UTC (permalink / raw)
  To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw

You could try running epubcheck on the epub produced by pandoc, to see if it points to anything.


> On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss <pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> 
> I just did some further testing, and replaced the sections that I would otherwise have removed with as many words and paragraphs, but no signs, only "test test test" etc. The document then works. So I was wrong about the length: It must be some character or symbol producing the error (only with pandoc, not other EPUB converters). Any idea how to further isolate it, or how to circumvent with a pandoc command or template?
> 
> Thanks for the help so far, Bernardo.
> 
> 
> 
> mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
> I am not sure what you mean by normalize in this context. I'll elaborate in case this is what you mean: In the interest of removing variables that might interfere with troubleshooting, I have copied the text from research papers (not just one, but a few), pasted it in notepad, copied and pasted it back into a new word-file (this is more thorough than "clear formatting"), ran this "pure" file through pandoc and I get the error. If I then randomly shorten the file, the error disappears. This is not the case for my "test" file, but only for research papers, which is baffling. I can only assume that pandoc responds to something like a character or in-text references in particular contexts, or as was my original hypothesis, the number of lines or columns in the EPUB. 
> 
> mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
> Have you tried editing the original research paper in some minor way (adding or removing a couple of characters) and then running it? This is a completely wild guess, but maybe the text in the file is getting normalized upon editing them, whereas the original research paper still contains the unedited, unnormalized text.
> 
> On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> I thank you for the suggestion. It is proving somewhat hard to (dis)confirm. I have made a testfile with just the word "test" pasted over and over again, with and without various formatting and with the same length or longer as the proper papers. This file consistently works. But when I attempt to do it with a regular research paper, it only works if I shorten it. Curiously, I can remove either half of the main text, or indeed sections here and there, randomly, and it works, but not with all of them present. I have combed it for special characters or tags, but cannot find any. 
> 
> mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. Vasconcelos:
> I do not know the answer to this problem in particular, but perhaps it is worth checking the main document and the bibliography for invisible control characters (e.g. `\X{A0}`). They tend to cause all sorts of strange problems that result in random error msgs.
> 
> On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
> We have a workflow in Open Journal Systems where we use Pandoc to convert word documents to EPUB, and then display them with an embedded EPUB app (Bibi). 
> 
> Our resulting EPUBs work fine with both debuggers and viewers like calibre. They work in Bibi, but only when they are reduced to a certain length. Whenever the files exceed approx 100 lines or 600 words, Bibi claims:
> 
> TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
> 
> Meanwhile, the same documents works when converted to EPUB using other converters, or when I reduce the length (length, not size in bytes-- I've tried with graphics, still works). It suddenly works when I reduce the length by removing pure paragraph text, even though all the formatted elements (abstract, references, etc) are the same. 
> 
> I recognize that this problem is very specific to the interrelation pandoc <-> Bibi, but I'd be grateful for general troubleshooting suggestions. 
> 
> Thanks in advance, 
> 
> Peter
> 
> 
> -- 
> You received this message because you are subscribed to a topic in the Google Groups "pandoc-discuss" group.
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> 
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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                         ` <0AFB3E23-B7C1-49E8-9F8A-12716F6A2C40-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
@ 2023-02-27 16:22                           ` 'Peter Vedal Utnes' via pandoc-discuss
       [not found]                             ` <20942a45-0995-4a50-888a-cf25e9895920n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 16:22 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 7484 bytes --]

I have now done the elimination process, as suggested by Bastien, of 
replacing the working file, which was the EPUB of the research paper where 
I had swapped paragraphs 2-10 with "test test test", with the original 
paragraphs from the paper. It worked until I tried to restore a sentence in 
the middle of paragraph 3, going from above, or paragraph 6, going from 
below. When I insert the next sentence in either end, the document fails to 
convert (in a manner readable by bibi epub viewer). There does not seem to 
be unicode characters that might interfere. I have ran the debugger you 
suggest, John ,and there are indeed errors (metadata not filled in and a 
missing tag end) but I fixing these do not seem to work. 

Here are the seemingly innocuous sentences that fail from above and below, 
respectively: 1)  Over years I have experienced much Bronze in the form of 
articles in toll access (TA) journals that have been made freely available 
for reading – not open access, but “Free access” as some publishers call it. 
2) One thing is to help editors to become aware of the issue, another is to 
find practical solutions for them to transition their scholarly content to 
OA – the rest of their content is really not of interest to us.

There seem to issues with a few other sentences in those 3 paragraphs too, 
but I can't see a pattern. 
Here is the article in question, though it is only the PDF galley, my EPUB 
testing is on a private server: 
https://septentrio.uit.no/index.php/nopos/article/view/6665



mandag 27. februar 2023 kl. 17:08:31 UTC+1 skrev John MacFarlane:

> You could try running epubcheck on the epub produced by pandoc, to see if 
> it points to anything.
>
>
> > On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss <
> pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> > 
> > I just did some further testing, and replaced the sections that I would 
> otherwise have removed with as many words and paragraphs, but no signs, 
> only "test test test" etc. The document then works. So I was wrong about 
> the length: It must be some character or symbol producing the error (only 
> with pandoc, not other EPUB converters). Any idea how to further isolate 
> it, or how to circumvent with a pandoc command or template?
> > 
> > Thanks for the help so far, Bernardo.
> > 
> > 
> > 
> > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
> > I am not sure what you mean by normalize in this context. I'll elaborate 
> in case this is what you mean: In the interest of removing variables that 
> might interfere with troubleshooting, I have copied the text from research 
> papers (not just one, but a few), pasted it in notepad, copied and pasted 
> it back into a new word-file (this is more thorough than "clear 
> formatting"), ran this "pure" file through pandoc and I get the error. If I 
> then randomly shorten the file, the error disappears. This is not the case 
> for my "test" file, but only for research papers, which is baffling. I can 
> only assume that pandoc responds to something like a character or in-text 
> references in particular contexts, or as was my original hypothesis, the 
> number of lines or columns in the EPUB. 
> > 
> > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
> > Have you tried editing the original research paper in some minor way 
> (adding or removing a couple of characters) and then running it? This is a 
> completely wild guess, but maybe the text in the file is getting normalized 
> upon editing them, whereas the original research paper still contains the 
> unedited, unnormalized text.
> > 
> > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <
> pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> > I thank you for the suggestion. It is proving somewhat hard to 
> (dis)confirm. I have made a testfile with just the word "test" pasted over 
> and over again, with and without various formatting and with the same 
> length or longer as the proper papers. This file consistently works. But 
> when I attempt to do it with a regular research paper, it only works if I 
> shorten it. Curiously, I can remove either half of the main text, or indeed 
> sections here and there, randomly, and it works, but not with all of them 
> present. I have combed it for special characters or tags, but cannot find 
> any. 
> > 
> > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. 
> Vasconcelos:
> > I do not know the answer to this problem in particular, but perhaps it 
> is worth checking the main document and the bibliography for invisible 
> control characters (e.g. `\X{A0}`). They tend to cause all sorts of strange 
> problems that result in random error msgs.
> > 
> > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
> > We have a workflow in Open Journal Systems where we use Pandoc to 
> convert word documents to EPUB, and then display them with an embedded EPUB 
> app (Bibi). 
> > 
> > Our resulting EPUBs work fine with both debuggers and viewers like 
> calibre. They work in Bibi, but only when they are reduced to a certain 
> length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
> claims:
> > 
> > TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
> > 
> > Meanwhile, the same documents works when converted to EPUB using other 
> converters, or when I reduce the length (length, not size in bytes-- I've 
> tried with graphics, still works). It suddenly works when I reduce the 
> length by removing pure paragraph text, even though all the formatted 
> elements (abstract, references, etc) are the same. 
> > 
> > I recognize that this problem is very specific to the interrelation 
> pandoc <-> Bibi, but I'd be grateful for general troubleshooting 
> suggestions. 
> > 
> > Thanks in advance, 
> > 
> > Peter
> > 
> > 
> > -- 
> > You received this message because you are subscribed to a topic in the 
> Google Groups "pandoc-discuss" group.
> > To unsubscribe from this topic, visit 
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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                             ` <20942a45-0995-4a50-888a-cf25e9895920n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 16:39                               ` Bastien DUMONT
  2023-02-27 16:49                                 ` 'Peter Vedal Utnes' via pandoc-discuss
  0 siblings, 1 reply; 14+ messages in thread
From: Bastien DUMONT @ 2023-02-27 16:39 UTC (permalink / raw)
  To: 'Peter Vedal Utnes' via pandoc-discuss

If you narrow down the document to the offending sentences (or only one of them), does bibi fail to read the resulting EPUB? Such minimal source and EPUB documents would be easier to inspect, and the latter could even be included in a bug report for bibi.

Le Monday 27 February 2023 à 08:22:34AM, 'Peter Vedal Utnes' via pandoc-discuss a écrit :
> I have now done the elimination process, as suggested by Bastien, of replacing
> the working file, which was the EPUB of the research paper where I had swapped
> paragraphs 2-10 with "test test test", with the original paragraphs from the
> paper. It worked until I tried to restore a sentence in the middle of paragraph
> 3, going from above, or paragraph 6, going from below. When I insert the next
> sentence in either end, the document fails to convert (in a manner readable by
> bibi epub viewer). There does not seem to be unicode characters that might
> interfere. I have ran the debugger you suggest, John ,and there are indeed
> errors (metadata not filled in and a missing tag end) but I fixing these do not
> seem to work. 
> 
> Here are the seemingly innocuous sentences that fail from above and below,
> respectively: 1)  Over years I have experienced much Bronze in the form of
> articles in toll access (TA) journals that have been made freely available for
> reading – not open access, but “Free access” as some publishers call it. 2) One
> thing is to help editors to become aware of the issue, another is to find
> practical solutions for them to transition their scholarly content to OA – the
> rest of their content is really not of interest to us.
> 
> There seem to issues with a few other sentences in those 3 paragraphs too, but
> I can't see a pattern. 
> Here is the article in question, though it is only the PDF galley, my EPUB
> testing is on a private server: https://septentrio.uit.no/index.php/nopos/
> article/view/6665
> 
> 
> 
> mandag 27. februar 2023 kl. 17:08:31 UTC+1 skrev John MacFarlane:
> 
>     You could try running epubcheck on the epub produced by pandoc, to see if
>     it points to anything.
> 
> 
>     > On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss <
>     pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>     >
>     > I just did some further testing, and replaced the sections that I would
>     otherwise have removed with as many words and paragraphs, but no signs,
>     only "test test test" etc. The document then works. So I was wrong about
>     the length: It must be some character or symbol producing the error (only
>     with pandoc, not other EPUB converters). Any idea how to further isolate
>     it, or how to circumvent with a pandoc command or template?
>     >
>     > Thanks for the help so far, Bernardo.
>     >
>     >
>     >
>     > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
>     > I am not sure what you mean by normalize in this context. I'll elaborate
>     in case this is what you mean: In the interest of removing variables that
>     might interfere with troubleshooting, I have copied the text from research
>     papers (not just one, but a few), pasted it in notepad, copied and pasted
>     it back into a new word-file (this is more thorough than "clear
>     formatting"), ran this "pure" file through pandoc and I get the error. If I
>     then randomly shorten the file, the error disappears. This is not the case
>     for my "test" file, but only for research papers, which is baffling. I can
>     only assume that pandoc responds to something like a character or in-text
>     references in particular contexts, or as was my original hypothesis, the
>     number of lines or columns in the EPUB.
>     >
>     > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev bernardov...@gmail.com:
>     > Have you tried editing the original research paper in some minor way
>     (adding or removing a couple of characters) and then running it? This is a
>     completely wild guess, but maybe the text in the file is getting normalized
>     upon editing them, whereas the original research paper still contains the
>     unedited, unnormalized text.
>     >
>     > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via pandoc-discuss <
>     pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>     > I thank you for the suggestion. It is proving somewhat hard to (dis)
>     confirm. I have made a testfile with just the word "test" pasted over and
>     over again, with and without various formatting and with the same length or
>     longer as the proper papers. This file consistently works. But when I
>     attempt to do it with a regular research paper, it only works if I shorten
>     it. Curiously, I can remove either half of the main text, or indeed
>     sections here and there, randomly, and it works, but not with all of them
>     present. I have combed it for special characters or tags, but cannot find
>     any.
>     >
>     > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
>     Vasconcelos:
>     > I do not know the answer to this problem in particular, but perhaps it is
>     worth checking the main document and the bibliography for invisible control
>     characters (e.g. `\X{A0}`). They tend to cause all sorts of strange
>     problems that result in random error msgs.
>     >
>     > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes wrote:
>     > We have a workflow in Open Journal Systems where we use Pandoc to convert
>     word documents to EPUB, and then display them with an embedded EPUB app
>     (Bibi).
>     >
>     > Our resulting EPUBs work fine with both debuggers and viewers like
>     calibre. They work in Bibi, but only when they are reduced to a certain
>     length. Whenever the files exceed approx 100 lines or 600 words, Bibi
>     claims:
>     >
>     > TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
>     >
>     > Meanwhile, the same documents works when converted to EPUB using other
>     converters, or when I reduce the length (length, not size in bytes-- I've
>     tried with graphics, still works). It suddenly works when I reduce the
>     length by removing pure paragraph text, even though all the formatted
>     elements (abstract, references, etc) are the same.
>     >
>     > I recognize that this problem is very specific to the interrelation
>     pandoc <-> Bibi, but I'd be grateful for general troubleshooting
>     suggestions.
>     >
>     > Thanks in advance,
>     >
>     > Peter
>     >
>     >
>     > --
>     > You received this message because you are subscribed to a topic in the
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> 
> 
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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
  2023-02-27 16:39                               ` Bastien DUMONT
@ 2023-02-27 16:49                                 ` 'Peter Vedal Utnes' via pandoc-discuss
       [not found]                                   ` <a484697f-9076-4a13-acf1-a645fa611614n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-27 16:49 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 9756 bytes --]

When I convert and try to publish a document with only the offending 
sentences, it does indeed fail, Bastien. Even when the document is 
otherwise empty. It is hard to see what might be causing this. I will have 
to continue the elimination down to the word, but I've been at this for 
nine hours and it is getting late. Will do that tomorrow. Meanwhile, thanks 
for the help, all of you. 


mandag 27. februar 2023 kl. 17:41:58 UTC+1 skrev Bastien DUMONT:

> If you narrow down the document to the offending sentences (or only one of 
> them), does bibi fail to read the resulting EPUB? Such minimal source and 
> EPUB documents would be easier to inspect, and the latter could even be 
> included in a bug report for bibi.
>
> Le Monday 27 February 2023 à 08:22:34AM, 'Peter Vedal Utnes' via 
> pandoc-discuss a écrit :
> > I have now done the elimination process, as suggested by Bastien, of 
> replacing
> > the working file, which was the EPUB of the research paper where I had 
> swapped
> > paragraphs 2-10 with "test test test", with the original paragraphs from 
> the
> > paper. It worked until I tried to restore a sentence in the middle of 
> paragraph
> > 3, going from above, or paragraph 6, going from below. When I insert the 
> next
> > sentence in either end, the document fails to convert (in a manner 
> readable by
> > bibi epub viewer). There does not seem to be unicode characters that 
> might
> > interfere. I have ran the debugger you suggest, John ,and there are 
> indeed
> > errors (metadata not filled in and a missing tag end) but I fixing these 
> do not
> > seem to work. 
> > 
> > Here are the seemingly innocuous sentences that fail from above and 
> below,
> > respectively: 1)  Over years I have experienced much Bronze in the form 
> of
> > articles in toll access (TA) journals that have been made freely 
> available for
> > reading – not open access, but “Free access” as some publishers call it. 
> 2) One
> > thing is to help editors to become aware of the issue, another is to find
> > practical solutions for them to transition their scholarly content to OA 
> – the
> > rest of their content is really not of interest to us.
> > 
> > There seem to issues with a few other sentences in those 3 paragraphs 
> too, but
> > I can't see a pattern. 
> > Here is the article in question, though it is only the PDF galley, my 
> EPUB
> > testing is on a private server: 
> https://septentrio.uit.no/index.php/nopos/
> > article/view/6665
> > 
> > 
> > 
> > mandag 27. februar 2023 kl. 17:08:31 UTC+1 skrev John MacFarlane:
> > 
> > You could try running epubcheck on the epub produced by pandoc, to see if
> > it points to anything.
> > 
> > 
> > > On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss <
> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> > >
> > > I just did some further testing, and replaced the sections that I would
> > otherwise have removed with as many words and paragraphs, but no signs,
> > only "test test test" etc. The document then works. So I was wrong about
> > the length: It must be some character or symbol producing the error (only
> > with pandoc, not other EPUB converters). Any idea how to further isolate
> > it, or how to circumvent with a pandoc command or template?
> > >
> > > Thanks for the help so far, Bernardo.
> > >
> > >
> > >
> > > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
> > > I am not sure what you mean by normalize in this context. I'll 
> elaborate
> > in case this is what you mean: In the interest of removing variables that
> > might interfere with troubleshooting, I have copied the text from 
> research
> > papers (not just one, but a few), pasted it in notepad, copied and pasted
> > it back into a new word-file (this is more thorough than "clear
> > formatting"), ran this "pure" file through pandoc and I get the error. 
> If I
> > then randomly shorten the file, the error disappears. This is not the 
> case
> > for my "test" file, but only for research papers, which is baffling. I 
> can
> > only assume that pandoc responds to something like a character or in-text
> > references in particular contexts, or as was my original hypothesis, the
> > number of lines or columns in the EPUB.
> > >
> > > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev 
> bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
> > > Have you tried editing the original research paper in some minor way
> > (adding or removing a couple of characters) and then running it? This is 
> a
> > completely wild guess, but maybe the text in the file is getting 
> normalized
> > upon editing them, whereas the original research paper still contains the
> > unedited, unnormalized text.
> > >
> > > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via 
> pandoc-discuss <
> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
> > > I thank you for the suggestion. It is proving somewhat hard to (dis)
> > confirm. I have made a testfile with just the word "test" pasted over and
> > over again, with and without various formatting and with the same length 
> or
> > longer as the proper papers. This file consistently works. But when I
> > attempt to do it with a regular research paper, it only works if I 
> shorten
> > it. Curiously, I can remove either half of the main text, or indeed
> > sections here and there, randomly, and it works, but not with all of them
> > present. I have combed it for special characters or tags, but cannot find
> > any.
> > >
> > > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
> > Vasconcelos:
> > > I do not know the answer to this problem in particular, but perhaps it 
> is
> > worth checking the main document and the bibliography for invisible 
> control
> > characters (e.g. `\X{A0}`). They tend to cause all sorts of strange
> > problems that result in random error msgs.
> > >
> > > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes 
> wrote:
> > > We have a workflow in Open Journal Systems where we use Pandoc to 
> convert
> > word documents to EPUB, and then display them with an embedded EPUB app
> > (Bibi).
> > >
> > > Our resulting EPUBs work fine with both debuggers and viewers like
> > calibre. They work in Bibi, but only when they are reduced to a certain
> > length. Whenever the files exceed approx 100 lines or 600 words, Bibi
> > claims:
> > >
> > > TypeError: Cannot read properties of undefined (reading ‘getAttribute’)
> > >
> > > Meanwhile, the same documents works when converted to EPUB using other
> > converters, or when I reduce the length (length, not size in bytes-- I've
> > tried with graphics, still works). It suddenly works when I reduce the
> > length by removing pure paragraph text, even though all the formatted
> > elements (abstract, references, etc) are the same.
> > >
> > > I recognize that this problem is very specific to the interrelation
> > pandoc <-> Bibi, but I'd be grateful for general troubleshooting
> > suggestions.
> > >
> > > Thanks in advance,
> > >
> > > Peter
> > >
> > >
> > > --
> > > You received this message because you are subscribed to a topic in the
> > Google Groups "pandoc-discuss" group.
> > > To unsubscribe from this topic, visit [1]https://groups.google.com/d/
> > topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe.
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> > pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
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> https://groups.google.com/d/
> > msgid/pandoc-discuss/
> > 4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com.
> > >
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> > 
> > 
> > --
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> an email
> > to [4]pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
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> https://groups.google.com/d/msgid/
> > pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%40googlegroups.com.
> > 
> > References:
> > 
> > [1] 
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> > [2] 
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> > [3] 
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> > [5] 
> https://groups.google.com/d/msgid/pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%40googlegroups.com?utm_medium=email&utm_source=footer
>
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[-- Attachment #1.2: Type: text/html, Size: 15314 bytes --]

^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                                   ` <a484697f-9076-4a13-acf1-a645fa611614n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
@ 2023-02-27 17:10                                     ` 'William Lupton' via pandoc-discuss
       [not found]                                       ` <CAEe_xxhpYFisSG6gMHRx=adVbGWOLGyS30t2G6VqnX7Sye1GEQ-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
  0 siblings, 1 reply; 14+ messages in thread
From: 'William Lupton' via pandoc-discuss @ 2023-02-27 17:10 UTC (permalink / raw)
  To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw

[-- Attachment #1: Type: text/plain, Size: 11777 bytes --]

Maybe this too obvious a comment, but it couldn't be the em-dashes could
it? Both your sentences below appear to have em-dashes. Try replacing them
with hyphens?

1) Over years I have experienced much Bronze in the form of articles in
toll access (TA) journals that have been made freely available for reading
– not open access, but “Free access” as some publishers call it. 2) One
thing is to help editors to become aware of the issue, another is to find
practical solutions for them to transition their scholarly content to OA –
the rest of their content is really not of interest to us.

-->

1) Over years I have experienced much Bronze in the form of articles in
toll access (TA) journals that have been made freely available for reading
- not open access, but “Free access” as some publishers call it. 2) One
thing is to help editors to become aware of the issue, another is to find
practical solutions for them to transition their scholarly content to OA -
the rest of their content is really not of interest to us.

On Mon, 27 Feb 2023 at 16:49, 'Peter Vedal Utnes' via pandoc-discuss <
pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:

> When I convert and try to publish a document with only the offending
> sentences, it does indeed fail, Bastien. Even when the document is
> otherwise empty. It is hard to see what might be causing this. I will have
> to continue the elimination down to the word, but I've been at this for
> nine hours and it is getting late. Will do that tomorrow. Meanwhile, thanks
> for the help, all of you.
>
>
> mandag 27. februar 2023 kl. 17:41:58 UTC+1 skrev Bastien DUMONT:
>
>> If you narrow down the document to the offending sentences (or only one
>> of them), does bibi fail to read the resulting EPUB? Such minimal source
>> and EPUB documents would be easier to inspect, and the latter could even be
>> included in a bug report for bibi.
>>
>> Le Monday 27 February 2023 à 08:22:34AM, 'Peter Vedal Utnes' via
>> pandoc-discuss a écrit :
>> > I have now done the elimination process, as suggested by Bastien, of
>> replacing
>> > the working file, which was the EPUB of the research paper where I had
>> swapped
>> > paragraphs 2-10 with "test test test", with the original paragraphs
>> from the
>> > paper. It worked until I tried to restore a sentence in the middle of
>> paragraph
>> > 3, going from above, or paragraph 6, going from below. When I insert
>> the next
>> > sentence in either end, the document fails to convert (in a manner
>> readable by
>> > bibi epub viewer). There does not seem to be unicode characters that
>> might
>> > interfere. I have ran the debugger you suggest, John ,and there are
>> indeed
>> > errors (metadata not filled in and a missing tag end) but I fixing
>> these do not
>> > seem to work.
>> >
>> > Here are the seemingly innocuous sentences that fail from above and
>> below,
>> > respectively: 1)  Over years I have experienced much Bronze in the form
>> of
>> > articles in toll access (TA) journals that have been made freely
>> available for
>> > reading – not open access, but “Free access” as some publishers call
>> it. 2) One
>> > thing is to help editors to become aware of the issue, another is to
>> find
>> > practical solutions for them to transition their scholarly content to
>> OA – the
>> > rest of their content is really not of interest to us.
>> >
>> > There seem to issues with a few other sentences in those 3 paragraphs
>> too, but
>> > I can't see a pattern.
>> > Here is the article in question, though it is only the PDF galley, my
>> EPUB
>> > testing is on a private server:
>> https://septentrio.uit.no/index.php/nopos/
>> > article/view/6665
>> >
>> >
>> >
>> > mandag 27. februar 2023 kl. 17:08:31 UTC+1 skrev John MacFarlane:
>> >
>> > You could try running epubcheck on the epub produced by pandoc, to see
>> if
>> > it points to anything.
>> >
>> >
>> > > On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss <
>> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>> > >
>> > > I just did some further testing, and replaced the sections that I
>> would
>> > otherwise have removed with as many words and paragraphs, but no signs,
>> > only "test test test" etc. The document then works. So I was wrong
>> about
>> > the length: It must be some character or symbol producing the error
>> (only
>> > with pandoc, not other EPUB converters). Any idea how to further
>> isolate
>> > it, or how to circumvent with a pandoc command or template?
>> > >
>> > > Thanks for the help so far, Bernardo.
>> > >
>> > >
>> > >
>> > > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes:
>> > > I am not sure what you mean by normalize in this context. I'll
>> elaborate
>> > in case this is what you mean: In the interest of removing variables
>> that
>> > might interfere with troubleshooting, I have copied the text from
>> research
>> > papers (not just one, but a few), pasted it in notepad, copied and
>> pasted
>> > it back into a new word-file (this is more thorough than "clear
>> > formatting"), ran this "pure" file through pandoc and I get the error.
>> If I
>> > then randomly shorten the file, the error disappears. This is not the
>> case
>> > for my "test" file, but only for research papers, which is baffling. I
>> can
>> > only assume that pandoc responds to something like a character or
>> in-text
>> > references in particular contexts, or as was my original hypothesis,
>> the
>> > number of lines or columns in the EPUB.
>> > >
>> > > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev
>> bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org:
>> > > Have you tried editing the original research paper in some minor way
>> > (adding or removing a couple of characters) and then running it? This
>> is a
>> > completely wild guess, but maybe the text in the file is getting
>> normalized
>> > upon editing them, whereas the original research paper still contains
>> the
>> > unedited, unnormalized text.
>> > >
>> > > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via
>> pandoc-discuss <
>> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>> > > I thank you for the suggestion. It is proving somewhat hard to (dis)
>> > confirm. I have made a testfile with just the word "test" pasted over
>> and
>> > over again, with and without various formatting and with the same
>> length or
>> > longer as the proper papers. This file consistently works. But when I
>> > attempt to do it with a regular research paper, it only works if I
>> shorten
>> > it. Curiously, I can remove either half of the main text, or indeed
>> > sections here and there, randomly, and it works, but not with all of
>> them
>> > present. I have combed it for special characters or tags, but cannot
>> find
>> > any.
>> > >
>> > > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A.
>> > Vasconcelos:
>> > > I do not know the answer to this problem in particular, but perhaps
>> it is
>> > worth checking the main document and the bibliography for invisible
>> control
>> > characters (e.g. `\X{A0}`). They tend to cause all sorts of strange
>> > problems that result in random error msgs.
>> > >
>> > > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes
>> wrote:
>> > > We have a workflow in Open Journal Systems where we use Pandoc to
>> convert
>> > word documents to EPUB, and then display them with an embedded EPUB app
>> > (Bibi).
>> > >
>> > > Our resulting EPUBs work fine with both debuggers and viewers like
>> > calibre. They work in Bibi, but only when they are reduced to a certain
>> > length. Whenever the files exceed approx 100 lines or 600 words, Bibi
>> > claims:
>> > >
>> > > TypeError: Cannot read properties of undefined (reading
>> ‘getAttribute’)
>> > >
>> > > Meanwhile, the same documents works when converted to EPUB using
>> other
>> > converters, or when I reduce the length (length, not size in bytes--
>> I've
>> > tried with graphics, still works). It suddenly works when I reduce the
>> > length by removing pure paragraph text, even though all the formatted
>> > elements (abstract, references, etc) are the same.
>> > >
>> > > I recognize that this problem is very specific to the interrelation
>> > pandoc <-> Bibi, but I'd be grateful for general troubleshooting
>> > suggestions.
>> > >
>> > > Thanks in advance,
>> > >
>> > > Peter
>> > >
>> > >
>> > > --
>> > > You received this message because you are subscribed to a topic in
>> the
>> > Google Groups "pandoc-discuss" group.
>> > > To unsubscribe from this topic, visit [1]https://groups.google.com/d/
>> > topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe.
>> > > To unsubscribe from this group and all its topics, send an email to
>> > pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> > > To view this discussion on the web visit [2]
>> https://groups.google.com/d/
>> > msgid/pandoc-discuss/
>> > 4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com.
>> > >
>> > > --
>> > > You received this message because you are subscribed to the Google
>> Groups
>> > "pandoc-discuss" group.
>> > > To unsubscribe from this group and stop receiving emails from it,
>> send an
>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> > > To view this discussion on the web visit [3]
>> https://groups.google.com/d/
>> > msgid/pandoc-discuss/
>> > bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com.
>> >
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> Groups
>> > "pandoc-discuss" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an email
>> > to [4]pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> > To view this discussion on the web visit [5]
>> https://groups.google.com/d/msgid/
>> > pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%40googlegroups.com.
>>
>> >
>> > References:
>> >
>> > [1]
>> https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe
>> > [2]
>> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com
>> > [3]
>> https://groups.google.com/d/msgid/pandoc-discuss/bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com
>> > [4] mailto:pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>> > [5]
>> https://groups.google.com/d/msgid/pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%40googlegroups.com?utm_medium=email&utm_source=footer
>>
>> --
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^ permalink raw reply	[flat|nested] 14+ messages in thread

* Re: Error caused by document length
       [not found]                                       ` <CAEe_xxhpYFisSG6gMHRx=adVbGWOLGyS30t2G6VqnX7Sye1GEQ-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
@ 2023-02-28 15:03                                         ` 'Peter Vedal Utnes' via pandoc-discuss
  0 siblings, 0 replies; 14+ messages in thread
From: 'Peter Vedal Utnes' via pandoc-discuss @ 2023-02-28 15:03 UTC (permalink / raw)
  To: pandoc-discuss


[-- Attachment #1.1: Type: text/plain, Size: 14209 bytes --]

I have resolved the issue by sidestepping it with the help of another OJS 
plugin that can also show embedded EPUBs (not on the list in OJS, but 
installed manually from Github, called epubjsviewer).

I will include some final remarks on my troubleshoting here, in case 
someone else searches this or a similar issue. As you can see above, in 
many of our research papers (formatted with word templates from various 
journals), Bibi epub viewer refuses to load some of the EPUBs unless you 
remove or replace certain paragraphs, even though these paragraphs are 
simply formatted with only <p> tags, and do not have special unicode 
characters or (e.g.) Norwegian letters (æøå). Neither is it related to 
in-text references, e.g. the --reference-list flag. It fails to load in 
Opera, Edge and some - but not all - versions of chrome. It is not related 
to formatting. The sections of the document that don't work, DO work if 
inserted into a non-pandoc generated EPUB. So there is some relation 
between the pandoc EPUB template and combinations of text that Bibi (the 
commonly used OJS epub viewer) does not tolerate. But it is not the NAV 
document nor the stylesheet, as I've replaced those to no avail. I have 
also tried numerous flags, such as --wrap, normalize, TOC levels, section 
divisions and so on, and of course all metadata. Further, it is troublesome 
to arrive at the specific text by the process of elimination, since there 
are evidently multiple sentences that fail. 

However, since the documents work in other viewers and are fine when 
debugged with EPUB check or Calibre, I have resorted to a different plugin 
for embedded EPUBs. I have learned a lot from the feedback here, and have 
improved our pandoc script, EPUB template and troubleshooting procedure. 

Thanks!

Peter

mandag 27. februar 2023 kl. 18:10:33 UTC+1 skrev William Lupton:

> Maybe this too obvious a comment, but it couldn't be the em-dashes could 
> it? Both your sentences below appear to have em-dashes. Try replacing them 
> with hyphens?
>
> 1) Over years I have experienced much Bronze in the form of articles in 
> toll access (TA) journals that have been made freely available for reading 
> – not open access, but “Free access” as some publishers call it. 2) One 
> thing is to help editors to become aware of the issue, another is to find 
> practical solutions for them to transition their scholarly content to OA – 
> the rest of their content is really not of interest to us.
>
> -->
>
> 1) Over years I have experienced much Bronze in the form of articles in 
> toll access (TA) journals that have been made freely available for reading 
> - not open access, but “Free access” as some publishers call it. 2) One 
> thing is to help editors to become aware of the issue, another is to find 
> practical solutions for them to transition their scholarly content to OA - 
> the rest of their content is really not of interest to us.
>
> On Mon, 27 Feb 2023 at 16:49, 'Peter Vedal Utnes' via pandoc-discuss <
> pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote:
>
>> When I convert and try to publish a document with only the offending 
>> sentences, it does indeed fail, Bastien. Even when the document is 
>> otherwise empty. It is hard to see what might be causing this. I will have 
>> to continue the elimination down to the word, but I've been at this for 
>> nine hours and it is getting late. Will do that tomorrow. Meanwhile, thanks 
>> for the help, all of you. 
>>
>>
>> mandag 27. februar 2023 kl. 17:41:58 UTC+1 skrev Bastien DUMONT:
>>
>>> If you narrow down the document to the offending sentences (or only one 
>>> of them), does bibi fail to read the resulting EPUB? Such minimal source 
>>> and EPUB documents would be easier to inspect, and the latter could even be 
>>> included in a bug report for bibi. 
>>>
>>> Le Monday 27 February 2023 à 08:22:34AM, 'Peter Vedal Utnes' via 
>>> pandoc-discuss a écrit : 
>>> > I have now done the elimination process, as suggested by Bastien, of 
>>> replacing 
>>> > the working file, which was the EPUB of the research paper where I had 
>>> swapped 
>>> > paragraphs 2-10 with "test test test", with the original paragraphs 
>>> from the 
>>> > paper. It worked until I tried to restore a sentence in the middle of 
>>> paragraph 
>>> > 3, going from above, or paragraph 6, going from below. When I insert 
>>> the next 
>>> > sentence in either end, the document fails to convert (in a manner 
>>> readable by 
>>> > bibi epub viewer). There does not seem to be unicode characters that 
>>> might 
>>> > interfere. I have ran the debugger you suggest, John ,and there are 
>>> indeed 
>>> > errors (metadata not filled in and a missing tag end) but I fixing 
>>> these do not 
>>> > seem to work.  
>>> > 
>>> > Here are the seemingly innocuous sentences that fail from above and 
>>> below, 
>>> > respectively: 1)  Over years I have experienced much Bronze in the 
>>> form of 
>>> > articles in toll access (TA) journals that have been made freely 
>>> available for 
>>> > reading – not open access, but “Free access” as some publishers call 
>>> it. 2) One 
>>> > thing is to help editors to become aware of the issue, another is to 
>>> find 
>>> > practical solutions for them to transition their scholarly content to 
>>> OA – the 
>>> > rest of their content is really not of interest to us. 
>>> > 
>>> > There seem to issues with a few other sentences in those 3 paragraphs 
>>> too, but 
>>> > I can't see a pattern.  
>>> > Here is the article in question, though it is only the PDF galley, my 
>>> EPUB 
>>> > testing is on a private server: 
>>> https://septentrio.uit.no/index.php/nopos/ 
>>> > article/view/6665 
>>> > 
>>> > 
>>> > 
>>> > mandag 27. februar 2023 kl. 17:08:31 UTC+1 skrev John MacFarlane: 
>>> > 
>>> > You could try running epubcheck on the epub produced by pandoc, to see 
>>> if 
>>> > it points to anything. 
>>> > 
>>> > 
>>> > > On Feb 27, 2023, at 6:33 AM, 'Peter Vedal Utnes' via pandoc-discuss 
>>> < 
>>> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote: 
>>> > > 
>>> > > I just did some further testing, and replaced the sections that I 
>>> would 
>>> > otherwise have removed with as many words and paragraphs, but no 
>>> signs, 
>>> > only "test test test" etc. The document then works. So I was wrong 
>>> about 
>>> > the length: It must be some character or symbol producing the error 
>>> (only 
>>> > with pandoc, not other EPUB converters). Any idea how to further 
>>> isolate 
>>> > it, or how to circumvent with a pandoc command or template? 
>>> > > 
>>> > > Thanks for the help so far, Bernardo. 
>>> > > 
>>> > > 
>>> > > 
>>> > > mandag 27. februar 2023 kl. 15:23:57 UTC+1 skrev Peter Vedal Utnes: 
>>> > > I am not sure what you mean by normalize in this context. I'll 
>>> elaborate 
>>> > in case this is what you mean: In the interest of removing variables 
>>> that 
>>> > might interfere with troubleshooting, I have copied the text from 
>>> research 
>>> > papers (not just one, but a few), pasted it in notepad, copied and 
>>> pasted 
>>> > it back into a new word-file (this is more thorough than "clear 
>>> > formatting"), ran this "pure" file through pandoc and I get the error. 
>>> If I 
>>> > then randomly shorten the file, the error disappears. This is not the 
>>> case 
>>> > for my "test" file, but only for research papers, which is baffling. I 
>>> can 
>>> > only assume that pandoc responds to something like a character or 
>>> in-text 
>>> > references in particular contexts, or as was my original hypothesis, 
>>> the 
>>> > number of lines or columns in the EPUB. 
>>> > > 
>>> > > mandag 27. februar 2023 kl. 15:17:10 UTC+1 skrev 
>>> bernardov...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org: 
>>> > > Have you tried editing the original research paper in some minor way 
>>> > (adding or removing a couple of characters) and then running it? This 
>>> is a 
>>> > completely wild guess, but maybe the text in the file is getting 
>>> normalized 
>>> > upon editing them, whereas the original research paper still contains 
>>> the 
>>> > unedited, unnormalized text. 
>>> > > 
>>> > > On Mon, Feb 27, 2023 at 10:48 AM 'Peter Vedal Utnes' via 
>>> pandoc-discuss < 
>>> > pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> wrote: 
>>> > > I thank you for the suggestion. It is proving somewhat hard to (dis) 
>>> > confirm. I have made a testfile with just the word "test" pasted over 
>>> and 
>>> > over again, with and without various formatting and with the same 
>>> length or 
>>> > longer as the proper papers. This file consistently works. But when I 
>>> > attempt to do it with a regular research paper, it only works if I 
>>> shorten 
>>> > it. Curiously, I can remove either half of the main text, or indeed 
>>> > sections here and there, randomly, and it works, but not with all of 
>>> them 
>>> > present. I have combed it for special characters or tags, but cannot 
>>> find 
>>> > any. 
>>> > > 
>>> > > mandag 27. februar 2023 kl. 13:49:58 UTC+1 skrev Bernardo C. D. A. 
>>> > Vasconcelos: 
>>> > > I do not know the answer to this problem in particular, but perhaps 
>>> it is 
>>> > worth checking the main document and the bibliography for invisible 
>>> control 
>>> > characters (e.g. `\X{A0}`). They tend to cause all sorts of strange 
>>> > problems that result in random error msgs. 
>>> > > 
>>> > > On Monday, February 27, 2023 at 8:16:20 AM UTC-3 Peter Vedal Utnes 
>>> wrote: 
>>> > > We have a workflow in Open Journal Systems where we use Pandoc to 
>>> convert 
>>> > word documents to EPUB, and then display them with an embedded EPUB 
>>> app 
>>> > (Bibi). 
>>> > > 
>>> > > Our resulting EPUBs work fine with both debuggers and viewers like 
>>> > calibre. They work in Bibi, but only when they are reduced to a 
>>> certain 
>>> > length. Whenever the files exceed approx 100 lines or 600 words, Bibi 
>>> > claims: 
>>> > > 
>>> > > TypeError: Cannot read properties of undefined (reading 
>>> ‘getAttribute’) 
>>> > > 
>>> > > Meanwhile, the same documents works when converted to EPUB using 
>>> other 
>>> > converters, or when I reduce the length (length, not size in bytes-- 
>>> I've 
>>> > tried with graphics, still works). It suddenly works when I reduce the 
>>> > length by removing pure paragraph text, even though all the formatted 
>>> > elements (abstract, references, etc) are the same. 
>>> > > 
>>> > > I recognize that this problem is very specific to the interrelation 
>>> > pandoc <-> Bibi, but I'd be grateful for general troubleshooting 
>>> > suggestions. 
>>> > > 
>>> > > Thanks in advance, 
>>> > > 
>>> > > Peter 
>>> > > 
>>> > > 
>>> > > -- 
>>> > > You received this message because you are subscribed to a topic in 
>>> the 
>>> > Google Groups "pandoc-discuss" group. 
>>> > > To unsubscribe from this topic, visit [1]
>>> https://groups.google.com/d/ 
>>> > topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe. 
>>> > > To unsubscribe from this group and all its topics, send an email to 
>>> > pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>>> > > To view this discussion on the web visit [2]
>>> https://groups.google.com/d/ 
>>> > msgid/pandoc-discuss/ 
>>> > 4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com. 
>>> > > 
>>> > > -- 
>>> > > You received this message because you are subscribed to the Google 
>>> Groups 
>>> > "pandoc-discuss" group. 
>>> > > To unsubscribe from this group and stop receiving emails from it, 
>>> send an 
>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>>> > > To view this discussion on the web visit [3]
>>> https://groups.google.com/d/ 
>>> > msgid/pandoc-discuss/ 
>>> > bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com. 
>>> > 
>>> > 
>>> > -- 
>>> > You received this message because you are subscribed to the Google 
>>> Groups 
>>> > "pandoc-discuss" group. 
>>> > To unsubscribe from this group and stop receiving emails from it, send 
>>> an email 
>>> > to [4]pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>>> > To view this discussion on the web visit [5]
>>> https://groups.google.com/d/msgid/ 
>>> > pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%
>>> 40googlegroups.com. 
>>> > 
>>> > References: 
>>> > 
>>> > [1] 
>>> https://groups.google.com/d/topic/pandoc-discuss/hPUa1uWGS_k/unsubscribe 
>>> > [2] 
>>> https://groups.google.com/d/msgid/pandoc-discuss/4bd152b5-32f7-4f4c-9a9b-0d20afebea84n%40googlegroups.com 
>>> > [3] 
>>> https://groups.google.com/d/msgid/pandoc-discuss/bc147d77-69c9-4e5d-82a6-e149f662a823n%40googlegroups.com 
>>> > [4] mailto:pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org 
>>> > [5] 
>>> https://groups.google.com/d/msgid/pandoc-discuss/20942a45-0995-4a50-888a-cf25e9895920n%40googlegroups.com?utm_medium=email&utm_source=footer 
>>>
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> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/pandoc-discuss/a484697f-9076-4a13-acf1-a645fa611614n%40googlegroups.com 
>> <https://groups.google.com/d/msgid/pandoc-discuss/a484697f-9076-4a13-acf1-a645fa611614n%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>

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2023-02-27 11:16 Error caused by document length 'Peter Vedal Utnes' via pandoc-discuss
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2023-02-27 12:49   ` Bernardo C. D. A. Vasconcelos
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2023-02-27 13:48       ` 'Peter Vedal Utnes' via pandoc-discuss
     [not found]         ` <4bd152b5-32f7-4f4c-9a9b-0d20afebea84n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2023-02-27 14:16           ` bernardovasconcelos-Re5JQEeQqe8AvxtiuMwx3w
     [not found]             ` <CAEJ71f529ORrJ+aaLU-8JFbE3uLvYkQdKcJjKSJb5mJSt+jOvA-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
2023-02-27 14:23               ` 'Peter Vedal Utnes' via pandoc-discuss
     [not found]                 ` <db7972f9-8881-4941-92ea-9b8f51c0c404n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2023-02-27 14:33                   ` 'Peter Vedal Utnes' via pandoc-discuss
     [not found]                     ` <bc147d77-69c9-4e5d-82a6-e149f662a823n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2023-02-27 14:54                       ` Bastien DUMONT
2023-02-27 15:45                         ` Bernardo C. D. A. Vasconcelos
2023-02-27 16:08                       ` John MacFarlane
     [not found]                         ` <0AFB3E23-B7C1-49E8-9F8A-12716F6A2C40-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
2023-02-27 16:22                           ` 'Peter Vedal Utnes' via pandoc-discuss
     [not found]                             ` <20942a45-0995-4a50-888a-cf25e9895920n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2023-02-27 16:39                               ` Bastien DUMONT
2023-02-27 16:49                                 ` 'Peter Vedal Utnes' via pandoc-discuss
     [not found]                                   ` <a484697f-9076-4a13-acf1-a645fa611614n-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
2023-02-27 17:10                                     ` 'William Lupton' via pandoc-discuss
     [not found]                                       ` <CAEe_xxhpYFisSG6gMHRx=adVbGWOLGyS30t2G6VqnX7Sye1GEQ-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
2023-02-28 15:03                                         ` 'Peter Vedal Utnes' via pandoc-discuss

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