URL in references (bibtex and yaml)

URL in references (bibtex and yaml)

[Piero Grandesso]

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I am just starting to learn bibtex so it could be my fault, but I am having 
problems with pandoc 2 and references that contain URLs. And the behavior 
differs between bibtex and yaml bibliographies.

A minimal example in markdown will compile correctly in HTML, given this 
bibliography:

```
@InCollection{item3,
author="John Doe and Jenny Roe",
title="Why Water Is Wet",
url="http://pandoc.org/",
booktitle="Third Book",
editor="Sam Smith",
publisher="Oxford University Press",
address="Oxford",
year="2007"
}
```

however when compiling in JATS XML the URL is handled wrongly:

```
<ref-list>
  <ref id="ref-1"><element-citation 
publication-type="bookchapter"><person-group 
person-group-type="author"><name><surname>Doe</surname>,
  <given-names>John</given-names></name>, <name><surname>Roe</surname>,
  <given-names>Jenny</given-names></name></person-group><article-title>Why
  water is wet</article-title><source>Third
  book</source><person-group 
person-group-type="editor"><name><surname>Smith</surname>,
  <given-names>Sam</given-names></name></person-group><publisher-name>Oxford
  University
  Press</publisher-name><publisher-loc>Oxford</publisher-loc><ext-link 
ext-link-type="uri" xlink:href="<ext-link ext-link-type="uri" 
xlink:href="http://pandoc.org/">http://pandoc.org/</ext-link>" 
xlink:type="simple"><ext-link ext-link-type="uri" 
xlink:href="http://pandoc.org/">http://pandoc.org/</ext-link></ext-link></element-citation></ref>
</ref-list>
```

Then I tried using the citation in YAML; maybe I am missing something, but 
the URL field in YAML reference is ignored (both in JATS XML and in HTML)

Here is the YAML, is there a different syntax?

---
references:
- id: item3
  type: chapter
  author:
  - family: Doe
    given: John
  - family: Roe
    given: Jenny
  editor:
  - family: Smith
    given: Sam
  issued:
  - year: '2007'
  title: Why water is wet
  container-title: Third book
  publisher: Oxford University Press
  publisher-place: Oxford
  url: 'http://pandoc.org/'
...

Thanks,
Piero

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Re: URL in references (bibtex and yaml)

[John MACFARLANE]

Try capitalizing: URL in the YAML.

By the way, `pandoc-citeproc -y mybib.bib` will give you a
YAML version of an existing bibtex bibliography.

Re: URL in references (bibtex and yaml)

[Piero Grandesso]

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Thanks, I didn't think of converting bib in YAML, capitalizing URL works 
correctly.

I can confirm that in both cases the JATS output is broken if URL is in a 
reference.

Piero

Il giorno mercoledì 8 novembre 2017 17:32:48 UTC+1, John MacFarlane ha 
scritto:
>
> Try capitalizing: URL in the YAML. 
>
> By the way, `pandoc-citeproc -y mybib.bib` will give you a 
> YAML version of an existing bibtex bibliography. 
>

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Re: URL in references (bibtex and yaml)

[John MacFarlane]

Can you explain what you mean? How is it broken? Given an
example?

+++ Piero Grandesso [Nov 10 17 00:30 ]:
>   I can confirm that in both cases the JATS output is broken if URL is in
>   a reference.

Re: URL in references (bibtex and yaml)

[Piero Grandesso]

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Sorry, it's in the first post but I didn't highlight the problem: 

the JATS writer print the URL of a reference wrongly (recursive?), the 
syntax is invalid

```
<ext-link ext-link-type="uri" xlink:href="<ext-link ext-link-type="uri" 
xlink:href="http://pandoc.org/">http://pandoc.org/</ext-link>" 
xlink:type="simple"><ext-link ext-link-type="uri" xlink:href="
http://pandoc.org/">http://pandoc.org/</ext-link></ext-link>
```

should be:

```
<ext-link ext-link-type="uri" xlink:href="http://pandoc.org/">
http://pandoc.org/</ext-link>
```

the DOI is handled correctly.


Il giorno sabato 11 novembre 2017 04:04:15 UTC+1, John MacFarlane ha 
scritto:
>
> Can you explain what you mean? How is it broken? Given an 
> example? 
>
> +++ Piero Grandesso [Nov 10 17 00:30 ]: 
> >   I can confirm that in both cases the JATS output is broken if URL is 
> in 
> >   a reference. 
>

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Re: URL in references (bibtex and yaml)

[John MacFarlane]

It has something to do with the special jats.csl we use if
no CSL is specified.  (If you use `--csl somenice.csl` on
the command line, you won't see this, but then you also
won't have the nice JATS bibliography.)

I'll look into it.

+++ Piero Grandesso [Nov 11 17 04:25 ]:
>   Sorry, it's in the first post but I didn't highlight the problem:
>   the JATS writer print the URL of a reference wrongly (recursive?), the
>   syntax is invalid
>   ```
>   <ext-link ext-link-type="uri" xlink:href="<ext-link ext-link-type="uri"
>   xlink:href="[1]http://pandoc.org/">[2]http://pandoc.org/</ext-link>"
>   xlink:type="simple"><ext-link ext-link-type="uri"
>   xlink:href="[3]http://pandoc.org/">[4]http://pandoc.org/</ext-link></ex
>   t-link>
>   ```
>   should be:
>   ```
>   <ext-link ext-link-type="uri"
>   xlink:href="[5]http://pandoc.org/">[6]http://pandoc.org/</ext-link>
>   ```
>   the DOI is handled correctly.
>   Il giorno sabato 11 novembre 2017 04:04:15 UTC+1, John MacFarlane ha
>   scritto:
>
>     Can you explain what you mean? How is it broken? Given an
>     example?
>     +++ Piero Grandesso [Nov 10 17 00:30 ]:
>     >   I can confirm that in both cases the JATS output is broken if
>     URL is in
>     >   a reference.
>
>   --
>   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 [7]pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>   To post to this group, send email to
>   [8]pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
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>   b809-081b57a2350c%40googlegroups.com.
>   For more options, visit [10]https://groups.google.com/d/optout.
>
>References
>
>   1. http://pandoc.org/
>   2. http://pandoc.org/
>   3. http://pandoc.org/
>   4. http://pandoc.org/
>   5. http://pandoc.org/
>   6. http://pandoc.org/
>   7. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   8. mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>   9. https://groups.google.com/d/msgid/pandoc-discuss/e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org?utm_medium=email&utm_source=footer
>  10. https://groups.google.com/d/optout

Re: URL in references (bibtex and yaml)

[John MacFarlane]

OK, I just fixed the problem in jats.csl.
Now we get:

<ref-list>
  <ref id="ref-1"><element-citation publication-type="bookchapter"><person-group person-group-type="author"><name><surname>Doe</surname>,
  <given-names>John</given-names></name>, <name><surname>Roe</surname>,
  <given-names>Jenny</given-names></name></person-group><article-title>Why
  water is wet</article-title><source>Third
  book</source><person-group person-group-type="editor"><name><surname>Smith</surname>,
  <given-names>Sam</given-names></name></person-group><publisher-name>Oxford
  University
  Press</publisher-name><publisher-loc>Oxford</publisher-loc><ext-link ext-link-type="uri" xlink:href="http://pandoc.org/">http://pandoc.org/</ext-link></element-citation></ref>
</ref-list>

If you don't want to rebuild pandoc, you can grab
data/jats.csl from the pandoc repository, and use
it on the command line with --csl jats.csl.

+++ John MacFarlane [Nov 11 17 16:02 ]:
>It has something to do with the special jats.csl we use if
>no CSL is specified.  (If you use `--csl somenice.csl` on
>the command line, you won't see this, but then you also
>won't have the nice JATS bibliography.)
>
>I'll look into it.
>
>+++ Piero Grandesso [Nov 11 17 04:25 ]:
>>  Sorry, it's in the first post but I didn't highlight the problem:
>>  the JATS writer print the URL of a reference wrongly (recursive?), the
>>  syntax is invalid
>>  ```
>>  <ext-link ext-link-type="uri" xlink:href="<ext-link ext-link-type="uri"
>>  xlink:href="[1]http://pandoc.org/">[2]http://pandoc.org/</ext-link>"
>>  xlink:type="simple"><ext-link ext-link-type="uri"
>>  xlink:href="[3]http://pandoc.org/">[4]http://pandoc.org/</ext-link></ex
>>  t-link>
>>  ```
>>  should be:
>>  ```
>>  <ext-link ext-link-type="uri"
>>  xlink:href="[5]http://pandoc.org/">[6]http://pandoc.org/</ext-link>
>>  ```
>>  the DOI is handled correctly.
>>  Il giorno sabato 11 novembre 2017 04:04:15 UTC+1, John MacFarlane ha
>>  scritto:
>>
>>    Can you explain what you mean? How is it broken? Given an
>>    example?
>>    +++ Piero Grandesso [Nov 10 17 00:30 ]:
>>    >   I can confirm that in both cases the JATS output is broken if
>>    URL is in
>>    >   a reference.
>>
>>  --
>>  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 [7]pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>  To post to this group, send email to
>>  [8]pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>  To view this discussion on the web visit
>>  [9]https://groups.google.com/d/msgid/pandoc-discuss/e63b4955-98ba-4f34-
>>  b809-081b57a2350c%40googlegroups.com.
>>  For more options, visit [10]https://groups.google.com/d/optout.
>>
>>References
>>
>>  1. http://pandoc.org/
>>  2. http://pandoc.org/
>>  3. http://pandoc.org/
>>  4. http://pandoc.org/
>>  5. http://pandoc.org/
>>  6. http://pandoc.org/
>>  7. mailto:pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>>  8. mailto:pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org
>>  9. https://groups.google.com/d/msgid/pandoc-discuss/e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org?utm_medium=email&utm_source=footer
>> 10. https://groups.google.com/d/optout
>
>-- 
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Re: URL in references (bibtex and yaml)

[Piero Grandesso]

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Thanks, it works now.
If another csl is specified in YAML it won't be taken into account when 
generating JATS. This is really nice as it allows workflows that involve 
multiple output formats.

Thanks for your work,
Piero

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