* URL in references (bibtex and yaml) @ 2017-11-08 10:41 Piero Grandesso [not found] ` <cffc5be7-654b-42a7-9e67-c23be85e4c5f-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: Piero Grandesso @ 2017-11-08 10:41 UTC (permalink / raw) To: pandoc-discuss [-- Attachment #1.1: Type: text/plain, Size: 2599 bytes --] 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 -- 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-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/cffc5be7-654b-42a7-9e67-c23be85e4c5f%40googlegroups.com. For more options, visit https://groups.google.com/d/optout. [-- Attachment #1.2: Type: text/html, Size: 432377 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <cffc5be7-654b-42a7-9e67-c23be85e4c5f-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <cffc5be7-654b-42a7-9e67-c23be85e4c5f-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> @ 2017-11-08 16:33 ` John MACFARLANE 2017-11-10 8:30 ` Piero Grandesso 0 siblings, 1 reply; 8+ messages in thread From: John MACFARLANE @ 2017-11-08 16:33 UTC (permalink / raw) To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw 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. ^ permalink raw reply [flat|nested] 8+ messages in thread
* Re: URL in references (bibtex and yaml) 2017-11-08 16:33 ` John MACFARLANE @ 2017-11-10 8:30 ` Piero Grandesso [not found] ` <1bea1195-3f10-4295-92fb-45fdc985c2aa-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: Piero Grandesso @ 2017-11-10 8:30 UTC (permalink / raw) To: pandoc-discuss [-- Attachment #1.1: Type: text/plain, Size: 1015 bytes --] 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. > -- 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-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/1bea1195-3f10-4295-92fb-45fdc985c2aa%40googlegroups.com. For more options, visit https://groups.google.com/d/optout. [-- Attachment #1.2: Type: text/html, Size: 430638 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <1bea1195-3f10-4295-92fb-45fdc985c2aa-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <1bea1195-3f10-4295-92fb-45fdc985c2aa-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> @ 2017-11-11 3:03 ` John MacFarlane [not found] ` <20171111030359.GH16934-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: John MacFarlane @ 2017-11-11 3:03 UTC (permalink / raw) To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw 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. ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <20171111030359.GH16934-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <20171111030359.GH16934-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> @ 2017-11-11 12:25 ` Piero Grandesso [not found] ` <e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: Piero Grandesso @ 2017-11-11 12:25 UTC (permalink / raw) To: pandoc-discuss [-- Attachment #1.1: Type: text/plain, Size: 1450 bytes --] 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. > -- 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-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/e63b4955-98ba-4f34-b809-081b57a2350c%40googlegroups.com. For more options, visit https://groups.google.com/d/optout. [-- Attachment #1.2: Type: text/html, Size: 431525 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> @ 2017-11-12 0:02 ` John MacFarlane [not found] ` <20171112000254.GA50577-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: John MacFarlane @ 2017-11-12 0:02 UTC (permalink / raw) To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw 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 ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <20171112000254.GA50577-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <20171112000254.GA50577-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> @ 2017-11-12 0:25 ` John MacFarlane [not found] ` <20171112002511.GA52781-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 0 siblings, 1 reply; 8+ messages in thread From: John MacFarlane @ 2017-11-12 0:25 UTC (permalink / raw) To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw 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 > >-- >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-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org >To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org >To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/20171112000254.GA50577%40MacBook-Air-2.local. >For more options, visit https://groups.google.com/d/optout. ^ permalink raw reply [flat|nested] 8+ messages in thread
[parent not found: <20171112002511.GA52781-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org>]
* Re: URL in references (bibtex and yaml) [not found] ` <20171112002511.GA52781-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> @ 2017-11-12 17:05 ` Piero Grandesso 0 siblings, 0 replies; 8+ messages in thread From: Piero Grandesso @ 2017-11-12 17:05 UTC (permalink / raw) To: pandoc-discuss [-- Attachment #1.1: Type: text/plain, Size: 795 bytes --] 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 -- 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-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/11b66d2c-4864-4196-9b2a-a44201f14403%40googlegroups.com. For more options, visit https://groups.google.com/d/optout. [-- Attachment #1.2: Type: text/html, Size: 429484 bytes --] ^ permalink raw reply [flat|nested] 8+ messages in thread
end of thread, other threads:[~2017-11-12 17:05 UTC | newest] Thread overview: 8+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 2017-11-08 10:41 URL in references (bibtex and yaml) Piero Grandesso [not found] ` <cffc5be7-654b-42a7-9e67-c23be85e4c5f-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 2017-11-08 16:33 ` John MACFARLANE 2017-11-10 8:30 ` Piero Grandesso [not found] ` <1bea1195-3f10-4295-92fb-45fdc985c2aa-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 2017-11-11 3:03 ` John MacFarlane [not found] ` <20171111030359.GH16934-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 2017-11-11 12:25 ` Piero Grandesso [not found] ` <e63b4955-98ba-4f34-b809-081b57a2350c-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org> 2017-11-12 0:02 ` John MacFarlane [not found] ` <20171112000254.GA50577-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 2017-11-12 0:25 ` John MacFarlane [not found] ` <20171112002511.GA52781-jF64zX8BO091tJRe0FUodcM6rOWSkUom@public.gmane.org> 2017-11-12 17:05 ` Piero Grandesso
This is a public inbox, see mirroring instructions for how to clone and mirror all data and code used for this inbox; as well as URLs for NNTP newsgroup(s).