Revise citeproc code to fit new citeproc 0.5 API.

Linkification of URLs in the bibliography is now done in
the citeproc library, depending on the setting of an option.
We set that option depending on the value of the metadata
field `link-bibliography` (defaulting to true, for consistency
with earlier behavior, though the new behavior includes the
CSL draft recommendation of hyperlinking the title or the whole
entry if a DOI, PMID, PMCID, or URL field is present but not
explicitly rendered).

These changes implement the following recommendations from the
draft CSL v1.0.2 spec (Appendix VI):

> The CSL syntax does not have support for configuration of links.
> However, processors should include links on bibliographic references,
> using the following rules:

> If the bibliography entry for an item renders any of the following
> identifiers, the identifier should be anchored as a link, with the
> target of the link as follows:

> - url: output as is
> - doi: prepend with "`https://doi.org/`"
> - pmid: prepend with "`https://www.ncbi.nlm.nih.gov/pubmed/`"
> - pmcid: prepend with "`https://www.ncbi.nlm.nih.gov/pmc/articles/`"

> If the identifier is rendered as a URI, include rendered URI components
> (e.g. "`https://doi.org/`") in the link anchor. Do not include any other
> affix text in the link anchor (e.g. "Available from: ", "doi: ", "PMID: ").
> If the bibliography entry for an item does not render any of
> the above identifiers, then set the anchor of the link as the item
> title. If title is not rendered, then set the anchor of the link as the
> full bibliography entry for the item. Set the target of the link as one
> of the following, in order of priority:
>
> - doi: prepend with "`https://doi.org/`"
> - pmcid: prepend with "`https://www.ncbi.nlm.nih.gov/pmc/articles/`"
> - pmid: prepend with "`https://www.ncbi.nlm.nih.gov/pubmed/`"
> - url: output as is
>
> If the item data does not include any of the above identifiers, do not
> include a link.
>
> Citation processors should include an option flag for calling
> applications to disable bibliography linking behavior.

Thanks to Benjamin Bray for getting this all working.
This commit is contained in:
John MacFarlane 2021-08-17 15:34:23 -07:00
parent 10dfd81000
commit fd99fe4d7e
7 changed files with 21 additions and 51 deletions

View file

@ -73,7 +73,9 @@ processCitations (Pandoc meta bs) = do
let linkCites = maybe False truish $ lookupMeta "link-citations" meta
let opts = defaultCiteprocOptions{ linkCitations = linkCites }
let linkBib = maybe True truish $ lookupMeta "link-bibliography" meta
let opts = defaultCiteprocOptions{ linkCitations = linkCites
, linkBibliography = linkBib }
let result = Citeproc.citeproc opts style mblang refs citations
mapM_ (report . CiteprocWarning) (resultWarnings result)
let sopts = styleOptions style
@ -105,8 +107,7 @@ processCitations (Pandoc meta bs) = do
$ cits
return $ walk removeQuoteSpan
$ Pandoc meta''
$ insertRefs refkvs classes meta''
(walk fixLinks $ B.toList bibs) bs'
$ insertRefs refkvs classes meta'' (B.toList bibs) bs'
removeQuoteSpan :: Inline -> Inline
removeQuoteSpan (Span ("",["csl-quoted"],[]) xs) = Span nullAttr xs
@ -210,7 +211,7 @@ getReferences mblocale (Pandoc meta bs) = do
Nothing -> return []
let addQuoteSpan (Quoted _ xs) = Span ("",["csl-quoted"],[]) xs
addQuoteSpan x = x
return $ map (linkifyVariables . legacyDateRanges . walk addQuoteSpan)
return $ map (legacyDateRanges . walk addQuoteSpan)
(externalRefs ++ inlineRefs)
-- note that inlineRefs can override externalRefs
@ -278,7 +279,7 @@ insertResolvedCitations (Cite cs ils) = do
[] -> return (Cite cs ils)
(x:xs) -> do
put xs
return $ Cite cs (walk fixLinks $ B.toList x)
return $ Cite cs (B.toList x)
insertResolvedCitations x = return x
getCitations :: Locale
@ -419,15 +420,6 @@ mvPunct moveNotes locale (Cite cs ils : Str "." : ys)
mvPunct moveNotes locale (x:xs) = x : mvPunct moveNotes locale xs
mvPunct _ _ [] = []
-- move https://doi.org etc. prefix inside link text (#6723):
fixLinks :: [Inline] -> [Inline]
fixLinks (Str t : Link attr [Str u1] (u2,tit) : xs)
| u2 == t <> u1
= Link attr [Str (t <> u1)] (u2,tit) : fixLinks xs
fixLinks (x:xs) = x : fixLinks xs
fixLinks [] = []
endWithPunct :: Bool -> [Inline] -> Bool
endWithPunct _ [] = False
endWithPunct onlyFinal xs@(_:_) =
@ -523,29 +515,6 @@ legacyDateRanges ref =
_ -> DateVal d
go x = x
linkifyVariables :: Reference Inlines -> Reference Inlines
linkifyVariables ref =
ref{ referenceVariables = M.mapWithKey go $ referenceVariables ref }
where
go "URL" x = tolink "https://" x
go "DOI" x = tolink "https://doi.org/" (fixShortDOI x)
go "ISBN" x = tolink "https://worldcat.org/isbn/" x
go "PMID" x = tolink "https://www.ncbi.nlm.nih.gov/pubmed/" x
go "PMCID" x = tolink "https://www.ncbi.nlm.nih.gov/pmc/articles/" x
go _ x = x
fixShortDOI x = let x' = extractText x
in if "10/" `T.isPrefixOf` x'
then TextVal $ T.drop 3 x'
-- see https://shortdoi.org
else TextVal x'
tolink pref x = let x' = extractText x
x'' = if "://" `T.isInfixOf` x'
then x'
else pref <> x'
in if T.null x'
then x
else FancyVal (B.link x'' "" (B.str x'))
extractText :: Val Inlines -> Text
extractText (TextVal x) = x
extractText (FancyVal x) = toText x

View file

@ -28,6 +28,7 @@ fromCslJson (CslSub x) = B.subscript (fromCslJson x)
fromCslJson (CslSup x) = B.superscript (fromCslJson x)
fromCslJson (CslNoCase x) = B.spanWith ("",["nocase"],[]) (fromCslJson x)
fromCslJson (CslDiv t x) = B.spanWith ("",["csl-" <> t],[]) (fromCslJson x)
fromCslJson (CslLink u x) = B.link u "" (fromCslJson x)
cslJsonToReferences :: ByteString -> Either String [Reference Inlines]
cslJsonToReferences raw =

View file

@ -54,7 +54,7 @@ import System.FilePath.Glob
import Text.DocTemplates (FromContext(lookupContext), Context)
import Text.DocLayout (literal)
import Text.TeXMath
import Text.Pandoc.Logging (LogMessage(TemplateWarning))
import Text.Pandoc.Logging (LogMessage(PowerpointTemplateWarning))
import Text.Pandoc.Writers.Math (convertMath)
import Text.Pandoc.Writers.Powerpoint.Presentation
import Text.Pandoc.Shared (tshow, stringify)
@ -457,11 +457,11 @@ presentationToArchive opts meta pres = do
<> "reference doc or in the default "
<> "reference doc included with pandoc."))
(Nothing, Just ((element, path, entry) :| _)) -> do
P.logOutput (PowerpointTemplateWarning
("Couldn't find layout named \""
<> layoutTitle <> "\" in provided "
<> "reference doc. Falling back to "
<> "the default included with pandoc."))
P.report (PowerpointTemplateWarning
("Couldn't find layout named \""
<> layoutTitle <> "\" in provided "
<> "reference doc. Falling back to "
<> "the default included with pandoc."))
pure SlideLayout { slElement = element
, slPath = path
, slEntry = entry

View file

@ -29,8 +29,9 @@ Foo.[^1] Bar.[^2] Baz.[^3]
::: {#refs .references .csl-bib-body}
::: {#ref-item1 .csl-entry}
Olson HA, 'Codes, Costs, and Critiques: The Organization of Information
in *Library Quarterly*, 1931--2004' (2006) 76 *Library Quarterly* 19
Olson HA, '[Codes, Costs, and Critiques: The Organization of Information
in *Library Quarterly*, 1931--2004](https://doi.org/10.1086/504343)'
(2006) 76 *Library Quarterly* 19
:::
::: {#ref-item2 .csl-entry}

View file

@ -44,8 +44,8 @@ I referenced something here^\[1\]^
::: {#refs .references .csl-bib-body}
::: {#ref-LiLiaoDongWanHaiYuDiQiDongWuCiJiShengChanLiYanJiuJiShengJingGuaYiXingPingJie2017 .csl-entry}
[\[1\] ]{.csl-left-margin}[李轶平, 于旭光, 孙明, 等.
辽东湾海域底栖动物次级生产力研究及生境适宜性评价\[J\]. 水产科学,
2017(06): 728--734.]{.csl-right-inline}
[辽东湾海域底栖动物次级生产力研究及生境适宜性评价](http://kns.cnki.net/kns/detail/detail.aspx?QueryID=4&CurRec=4&recid=&FileName=CHAN201706006&DbName=CJFDLAST2018&DbCode=CJFQ&yx=Y&pr=&URLID=21.1110.S.20171129.1725.006)\[J\].
水产科学, 2017(06): 728--734.]{.csl-right-inline}
:::
:::
```

View file

@ -28,8 +28,7 @@ references:
::: {#ref-item-1 .csl-entry}
[Wolfinger, Christine]{.smallcaps}: *Keine Angst vor Linux, Unix: ein
Lehrbuch für Linux- und Unix-Anwender*. 11., vollst. überarb. Aufl.
Aufl. Berlin \[u.a.\] : Springer Vieweg, 2013
--- ISBN [978-3-642-32078-1](https://worldcat.org/isbn/978-3-642-32078-1)
Aufl. Berlin \[u.a.\] : Springer Vieweg, 2013 --- ISBN 978-3-642-32078-1
:::
:::
```

View file

@ -28,8 +28,8 @@ references:
::: {#refs .references .csl-bib-body line-spacing="2"}
::: {#ref-ding_metallic_2012 .csl-entry}
[\[1\] ]{.csl-left-margin}[K. Ding, C. Z. Ning, *Light Sci. Appl.*
**2012**, *1*, e20.]{.csl-right-inline}
[[\[1\]K. Ding, C. Z. Ning, *Light Sci. Appl.* **2012**, *1*,
e20](https://doi.org/10.1038/lsa.2012.20)]{.csl-left-margin}.
:::
:::
```