How to disable links-as-notes in LaTeX bibliography

How to disable links-as-notes in LaTeX bibliography

[vinceroni]

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Hi all,

I have links-as-notes set to true in my Mardown YAML, but I would like to 
deactivate it for the bibliography: I want to avoid DOIs to create 
footnotes, it doesn't look that good.

I usually use pandoc-citeproc to process my bibliography when producing a 
PDF. So far, I have tried to modify the \newenvironment{cslreferences} 
comand in my LaTeX template, unsuccessfully. links-as-notes is defined 
using \DeclareRobustCommand, but I am not literate enough in LaTex to know 
if that is the source of my problem.

Any suggestion?

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Re: How to disable links-as-notes in LaTeX bibliography

[Albert Krewinkel]

vinceroni writes:

> I have links-as-notes set to true in my Mardown YAML, but I would like to
> deactivate it for the bibliography: I want to avoid DOIs to create
> footnotes, it doesn't look that good.

You could use a Lua filter to remove all links from the bibliography:

    -- filter which replaces all links with their text contents.
    local unlink = {
      Link = function (link) return link.content end
    }

    function Div (div)
      -- if we are looking at the bibliography, then traverse it and
      -- replace all links text.
      if div.identifier == 'refs' then
        return pandoc.utils.walk_block(div, unlink)
      end
    end

Save the above to a file `unlink-bib.lua` and pass it to pandoc with
`--lua-filter=unlink-bib.lua`. Make sure it option is positioned *after*
`--filter=pandoc-citeproc` for it to take effect.

--
Albert Krewinkel
GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124

Re: How to disable links-as-notes in LaTeX bibliography

[Benct Philip Jonsson]

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On 2020-04-22 14:17, Albert Krewinkel wrote:
> vinceroni writes:
> 
>> I have links-as-notes set to true in my Mardown YAML, but I would like to
>> deactivate it for the bibliography: I want to avoid DOIs to create
>> footnotes, it doesn't look that good.
> 
> You could use a Lua filter to remove all links from the bibliography:

You beat me to it! :-)

I have attached a filter of mine which turns links into notes containing 
a link with the URL as text, unless their URLs match certain patterns 
(which you can specify in the filter) or based on a class `.no-note` on 
the link, and conversely a class `.note` causes links with matching URLs 
to be turned into notes anyway.

I have already enabled a pattern matching `https://doi.org` in the filter.

Full (Markdown) documentation at the top of the file!


> 
>      -- filter which replaces all links with their text contents.
>      local unlink = {
>        Link = function (link) return link.content end
>      }
> 
>      function Div (div)
>        -- if we are looking at the bibliography, then traverse it and
>        -- replace all links text.
>        if div.identifier == 'refs' then
>          return pandoc.utils.walk_block(div, unlink)
>        end
>      end
> 
> Save the above to a file `unlink-bib.lua` and pass it to pandoc with
> `--lua-filter=unlink-bib.lua`. Make sure it option is positioned *after*
> `--filter=pandoc-citeproc` for it to take effect.
> 
> --
> Albert Krewinkel
> GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124
> 

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[-- Attachment #2: links-or-notes.lua --]
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--[======[
]======]


-- Set this to true to show URLs in notes as "<http://example.com>"
-- rather than as "http://example.com"
local note_url_brackets = false

-- This function turns a string into a pattern suitable for
-- matching (a prefix on) a URL.
-- *   By default the pattern is anchored to the start of the string.
--     Pass an explicit `false` as second argument to disable this.
-- *   By default the pattern is *not* anchored to the end of the string.
--     Pass an explicit `true` as third argument to enable final anchoring.

local function url_pattern (str, prefix, suffix)
  if nil == prefix then prefix = true end
  if 'string' == type(prefix) then
    prefix = '^' .. prefix .. '%:%/%/'
  else
    prefix = prefix and '^' or ""
  end
  suffix = suffix and '$' or ""
  local pattern = tostring(str)
    -- Escape punctuation characters
    :gsub('%p','%%%0')
  return prefix .. pattern .. suffix
end

------------------------------------------------------------
-- EXCEPTION URL PATTERNS
--
-- Edit as needed!
--
-- This table is a list of prefixes/patterns for
-- URLs which should not be turned into notes.
-- Basically domains.

local no_notes_urls = {
  '^%s*$', -- empty target
  url_pattern"https://doi.org", -- anchored
  -- url_pattern('wikipedia.org', false), -- unanchored
  -- url_pattern('example.com', 'https?') -- anchored and matches https OR http
}
------------------------------------------------------------

local url_str = note_url_brackets
  and
    function (url)
      url = '<' .. url .. '>'
      return pandoc.Str(url)
    end
  or
    pandoc.Str

function Link (link)
  if link.classes:includes"no-note" then return nil end
  local url = link.target
  if not link.classes:includes"note" then
    for _,pattern in ipairs(no_notes_urls) do
      if url:match(pattern) then return nil end
    end
  end
  url = url:gsub('^mailto%:',"")
  -- Already a textual URL?
  local str = pandoc.utils.stringify(link)
  if str:match( url_pattern(url,false) ) then return nil end
  local text = pandoc.List:new(link.content)
  link.content = {url_str(url)}
  text:extend{
    pandoc.Note{pandoc.Plain(link)}
  }
  link.classes:extend('no-note')
  return text
end

Re: How to disable links-as-notes in LaTeX bibliography

[Benct Philip Jonsson]

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I forgot to save the file before attaching it. Sorry! Correct version 
attached.

On 2020-04-22 14:59, Benct Philip Jonsson wrote:
> On 2020-04-22 14:17, Albert Krewinkel wrote:
>> vinceroni writes:
>>
>>> I have links-as-notes set to true in my Mardown YAML, but I would 
>>> like to
>>> deactivate it for the bibliography: I want to avoid DOIs to create
>>> footnotes, it doesn't look that good.
>>
>> You could use a Lua filter to remove all links from the bibliography:
> 
> You beat me to it! :-)
> 
> I have attached a filter of mine which turns links into notes containing 
> a link with the URL as text, unless their URLs match certain patterns 
> (which you can specify in the filter) or based on a class `.no-note` on 
> the link, and conversely a class `.note` causes links with matching URLs 
> to be turned into notes anyway.
> 
> I have already enabled a pattern matching `https://doi.org` in the filter.
> 
> Full (Markdown) documentation at the top of the file!
> 
> 
>>
>>      -- filter which replaces all links with their text contents.
>>      local unlink = {
>>        Link = function (link) return link.content end
>>      }
>>
>>      function Div (div)
>>        -- if we are looking at the bibliography, then traverse it and
>>        -- replace all links text.
>>        if div.identifier == 'refs' then
>>          return pandoc.utils.walk_block(div, unlink)
>>        end
>>      end
>>
>> Save the above to a file `unlink-bib.lua` and pass it to pandoc with
>> `--lua-filter=unlink-bib.lua`. Make sure it option is positioned *after*
>> `--filter=pandoc-citeproc` for it to take effect.
>>
>> -- 
>> Albert Krewinkel
>> GPG: 8eed e3e2 e8c5 6f18 81fe  e836 388d c0b2 1f63 1124
>>
> 

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[-- Attachment #2: links-or-notes.lua --]
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--[======[
# NAME

links-or-notes.lua - Pandoc filter for selectively *not* turning links
into notes.

# SYNOPSIS

    pandoc -L links-or-notes.lua ...

# IMPORTANT

Do *not* use `-V links-as-notes` or `-M links-as-notes` when using this
filter!

The filter *replaces* the functionality of that variable.

# DESCRIPTION

With Pandoc’s default templates for some formats you can set the
variable `-V links-as-notes` to get links rendered as footnotes. However
this allows for no exceptions: either *all* links are rendered as
footnotes or *no* links are rendered as footnotes. Sometimes you want
more granularity than that — typically you want links to some domains to
not be turned into footnotes, or you want to explicitly mark some links
as non-notes — and this filter allows for just that.

# USAGE

The filter provides two mechanisms for controlling which links are not
turned into footnotes:

1.  The filter contains an array table whose values are patterns for
    matching URLs. Any link with an URL which matches one of these
    patterns will not be turned into a note.

    There is a helper function `url_pattern` which turns an ordinary
    string into a suitable pattern for matching against a URL — it
    “protects” characters which are special in patterns so that they are
    matched as ordinary characters. Typically you just type something
    like this:

    ``` {.lua}
    local no_notes_url = {
      '^%s*$', -- empty target
      url_pattern"https://doi.org", -- anchored
      url_pattern('wikipedia.org', false), -- unanchored
      url_pattern('example.com', 'https?') -- anchored and
      -- matches https OR http
    }
    ```

    Each row in the table above — which you will find in the filter code
    below the line which says “EXCEPTION URL PATTERNS” — exemplifies a
    different way to generate a pattern matching an URL.

    1.  The first row is a “raw” pattern which will match a “blank” URL,
        so that you don’t get a blank footnote if you type something
        like `[blah]()` in your Markdown.

    2.  The second row matches any URL starting with `https://:doi.org`
        so that links with such URLs are not turned into footnotes. The
        actual pattern will be `^https%:%/%/doi%.org` with punctuation
        characters escaped and the leading `^` indicating that the match
        shall be anchored to the start of the URL. Such a pattern is
        created if the `url_pattern` is called with a single string
        argument: any punctuation characters in the string are escaped
        and the start-of-string anchor prepended.

    3.  The third row (which is actually disabled by default) matches
        any URL containing the substring `wikipedia.org`. Note that in
        this case the `url_pattern` function takes the boolean `false`
        as a second argument, which means that nothing is prepended to
        the pattern; the only action is that any punctuation characters
        in the string are escaped. Note also that when there are more
        than one argument (and the argument is not a string) the
        arguments must be put in parentheses. This omission of the
        anchor and the protocol is necessary because Wikipedia URLs are
        usually prefixed with a subdomain indicating the language, so
        that `https://en.wikipedia.org` links to the English Wikipedia,
        `https://sv.wikipedia.org` links to the Swedish Wikipedia and so
        on, and if you want Wikipedia URLs to be exempt from
        “notification” you probably want this regardless of the
        language!

    4.  In the fourth row — which is a pure throwaway example! — the
        second argument to `url_pattern` is a string. Such a string is
        used as the protocol of an anchored URL, so that the pattern
        becomes `^https?%:%/%/example%.org`. Note that the `?` after `s`
        is copied unescaped, which means that the `s` is optional, so
        that the pattern matches both `http://` and `https://` URLs!

2.  Any link with a class `.no-note` —
    e.g. `[link     text](http://example.com){.no-note}` — will not be
    turned into a link even if its URL does not match any of the
    exception patterns.

3.  Conversely any link with a class `.note` *will* be turned into a
    note even if its URL matches an exception pattern.

# TO BRACKET OR NOT TO BRACKET

There are two schools when it comes to presenting a literal URL in text:
either it is enclosed in angle brackets `<http://example.com>` or not
`http://example.com`. In the filter code there is a variable
`note_url_brackets`. If its value is `false` (the default) no brackets
are inserted by the filter. Change the value to `true` if you want
brackets inserted.

# A SPECIAL CASE: `mailto:` URLs.

As an exception a `mailto:` protocol is not included in the displayed
text when turning a link into a footnote.

# TODO

-   Take configuration from the document metadata.

# AUTHOR

Benct Philip Jonsson <bpjonsson+pandoc-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>

# COPYRIGHT AND LICENSE

This software is Copyright (c) 2020 by Benct Philip Jonsson.

This is free software, licensed under:

The MIT (X11) License

<http://www.opensource.org/licenses/mit-license.php>
]======]


-- Set this to true to show URLs in notes as "<http://example.com>"
-- rather than as "http://example.com"
local note_url_brackets = false

-- This function turns a string into a pattern suitable for
-- matching (a prefix on) a URL.
-- *   By default the pattern is anchored to the start of the string.
--     Pass an explicit `false` as second argument to disable this.
-- *   By default the pattern is *not* anchored to the end of the string.
--     Pass an explicit `true` as third argument to enable final anchoring.

local function url_pattern (str, prefix, suffix)
  if nil == prefix then prefix = true end
  if 'string' == type(prefix) then
    prefix = '^' .. prefix .. '%:%/%/'
  else
    prefix = prefix and '^' or ""
  end
  suffix = suffix and '$' or ""
  local pattern = tostring(str)
    -- Escape punctuation characters
    :gsub('%p','%%%0')
  return prefix .. pattern .. suffix
end

------------------------------------------------------------
-- EXCEPTION URL PATTERNS
--
-- Edit as needed!
--
-- This table is a list of prefixes/patterns for
-- URLs which should not be turned into notes.
-- Basically domains.

local no_notes_urls = {
  '^%s*$', -- empty target
  url_pattern"https://doi.org", -- anchored
  -- url_pattern('wikipedia.org', false), -- unanchored
  -- url_pattern('example.com', 'https?') -- anchored and matches https OR http
}
------------------------------------------------------------

local url_str = note_url_brackets
  and
    function (url)
      url = '<' .. url .. '>'
      return pandoc.Str(url)
    end
  or
    pandoc.Str

function Link (link)
  if link.classes:includes"no-note" then return nil end
  local url = link.target
  if not link.classes:includes"note" then
    for _,pattern in ipairs(no_notes_urls) do
      if url:match(pattern) then return nil end
    end
  end
  url = url:gsub('^mailto%:',"")
  -- Already a textual URL?
  local str = pandoc.utils.stringify(link)
  if str:match( url_pattern(url,false) ) then return nil end
  local text = pandoc.List:new(link.content)
  link.content = {url_str(url)}
  text:extend{
    pandoc.Note{pandoc.Plain(link)}
  }
  link.classes:extend('no-note')
  return text
end