Hacks to demo possible CiTO support

data/defaults/pdf.yaml

@@ -8,7 +8,7 @@ filters:
   - type: lua
     path: draft.lua
   - type: lua
-    path: self-citation.lua
+    path: insert-cito-in-ref.lua
 variables:
   # styling options
   colorlinks: true

data/filters/extract-cito.lua

@@ -0,0 +1,246 @@
+-- Copyright © 2017–2021 Albert Krewinkel, Robert Winkler
+--
+-- This library is free software; you can redistribute it and/or modify it
+-- under the terms of the MIT license. See LICENSE for details.
+
+local _version = '1.0.0'
+local properties_and_aliases = {
+  agreesWith = {
+    'agreeWith',
+    'agree_with',
+    'agrees_with',
+  },
+  citation = {
+  },
+  cites = {
+  },
+  citesAsAuthority = {
+    'asAuthority',
+    'cites_as_authority',
+    'as_authority',
+    'authority'
+  },
+  citesAsDataSource = {
+    "asDataSource",
+    "dataSource",
+    'cites_as_data_source',
+    "as_data_source",
+    "data_source"
+  },
+  citesAsEvidence = {
+    'asEvidence',
+    'cites_as_evidence',
+    'as_evidence',
+    'evidence'
+  },
+  citesAsMetadataDocument = {
+    'asMetadataDocument',
+    'metadataDocument',
+    'cites_as_metadata_document',
+    'as_metadata_document',
+    'metadata_document',
+    'metadata'
+  },
+  citesAsPotentialSolution = {
+    'cites_as_potential_solution',
+    'potentialSolution',
+    'potential_solution',
+    'solution'
+  },
+  citesAsRecommendedReading = {
+    'asRecommendedReading',
+    'recommendedReading',
+    'cites_as_recommended_reading',
+    'as_recommended_reading',
+    'recommended_reading'
+  },
+  citesAsRelated = {
+    'cites_as_related',
+    'related',
+  },
+  citesAsSourceDocument = {
+    'cites_as_source_document',
+    'sourceDocument',
+    'source_document'
+  },
+  citesForInformation = {
+    'cites_for_information',
+    'information',
+  },
+  compiles = {
+  },
+  confirms = {
+  },
+  containsAssertionFrom = {
+  },
+  corrects = {
+  },
+  credits = {
+  },
+  critiques = {
+  },
+  derides = {
+  },
+  describes = {
+  },
+  disagreesWith = {
+    'disagrees_with',
+    'disagree',
+    'disagrees'
+  },
+  discusses = {
+  },
+  disputes = {
+  },
+  documents = {
+  },
+  extends = {
+  },
+  includesExcerptFrom = {
+    'excerptFrom',
+    'excerpt',
+    'excerpt_from',
+    'includes_excerpt_from',
+  },
+  includesQuotationFrom = {
+    'quotationFrom',
+    'includes_quotation_from',
+    'quotation',
+    'quotation_from'
+  },
+  linksTo = {
+    'links_to',
+    'link'
+  },
+  obtainsBackgroundFrom = {
+    'backgroundFrom',
+    'obtains_background_from',
+    'background',
+    'background_from'
+  },
+  providesDataFor = {
+  },
+  obtainsSupportFrom = {
+  },
+  qualifies = {
+  },
+  parodies = {
+  },
+  refutes = {
+  },
+  repliesTo = {
+    'replies_to',
+  },
+  retracts = {
+  },
+  reviews = {
+  },
+  ridicules = {
+  },
+  speculatesOn = {
+  },
+  supports = {
+  },
+  updates = {
+  },
+  usesConclusionsFrom = {
+    'uses_conclusions_from'
+  },
+  usesDataFrom = {
+    'dataFrom',
+    'uses_data_from',
+    'data',
+    'data_from'
+  },
+  usesMethodIn = {
+    'methodIn',
+    'uses_method_in',
+    'method',
+    'method_in'
+  },
+}
+
+local default_cito_property = 'citation'
+
+--- Map from cito aliases to the actual cito property.
+local properties_by_alias = {}
+for property, aliases in pairs(properties_and_aliases) do
+  -- every property is an alias for itself
+  properties_by_alias[property] = property
+  for _, alias in pairs(aliases) do
+    properties_by_alias[alias] = property
+  end
+end
+
+--- Split citation ID into cito property and the actual citation ID. If
+--- the ID does not seem to contain a CiTO property, the
+--- `default_cito_property` will be returned, together with the
+--- unchanged input ID.
+local function split_cito_from_id (citation_id)
+  local split_citation_id = {}
+  local cito_props = {}
+  local id_started = false
+
+  for part in citation_id:gmatch('[^:]+') do
+    if not id_started and properties_by_alias[part] then
+      table.insert(cito_props, properties_by_alias[part])
+    else
+      id_started = true
+    end
+
+    if id_started then
+      table.insert(split_citation_id, 1, part)
+    end
+  end
+
+  if next(split_citation_id) == nill then
+    table.insert(split_citation_id, table.remove(cito_props))
+  end
+
+  return cito_props, table.concat(split_citation_id, ':')
+end
+
+--- CiTO properties by citation.
+local function store_cito (cito_cites, prop, cite_id)
+  if not prop then
+    return
+  end
+  if not cito_cites[cite_id] then
+    cito_cites[cite_id] = {}
+  end
+  table.insert(cito_cites[cite_id], prop)
+end
+
+
+--- Returns a Cite filter function which extracts CiTO information and
+--- add it to the given collection table.
+local function extract_cito (cito_cites)
+  return function (cite)
+    for k, citation in pairs(cite.citations) do
+      local cito_props, cite_id = split_cito_from_id(citation.id)
+      for l, cito_prop in pairs(cito_props) do
+        store_cito(cito_cites, cito_prop, cite_id)
+      end
+      citation.id = cite_id
+    end
+    return cite
+  end
+end
+
+--- Lists of citation IDs, indexed by CiTO properties.
+local properties_by_citation = {}
+
+return {
+  {
+    Cite = extract_cito(properties_by_citation)
+  },
+  {
+    Meta = function (meta)
+      meta.citation_properties = properties_by_citation
+      meta.bibliography = meta.bibliography or
+        meta.cito_bibliography or
+        meta['cito-bibliography']
+      return meta
+    end
+  }
+}

data/filters/insert-cito-in-ref.lua

@@ -0,0 +1,55 @@
+-- Copyright © 2021 Albert Krewinkel
+--
+-- This library is free software; you can redistribute it and/or modify it
+-- under the terms of the MIT license. See LICENSE for details.
+
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local citation_properties
+
+local function meta_citation_properties (meta)
+  citation_properties = meta.citation_properties
+end
+
+local function cito_properties(cite_id)
+  local props = citation_properties[cite_id]
+  if not props then return {} end
+
+  -- remove duplicates
+  local deduplicated_props = List()
+  local seen = {}
+  for _, prop in ipairs(props) do
+    if not seen[prop] then
+      deduplicated_props:insert(prop)
+      seen[prop] = true
+    end
+  end
+
+  return List(deduplicated_props):map(
+    function (x)
+      return pandoc.Strong{
+        pandoc.Space(),
+        pandoc.Str '[cito:',
+        pandoc.Str(utils.stringify(x)),
+        pandoc.Str ']'
+      }
+    end
+  )
+end
+
+local function add_cito (div)
+  local cite_id = div.identifier:match 'ref%-(.*)'
+  if cite_id and div.classes:includes 'csl-entry' then
+    for k, v in ipairs( div.content ) do
+        if k == 1 then
+          v.content:extend(cito_properties(cite_id))
+          return div
+        end
+    end
+  end
+end
+
+return {
+  {Meta = meta_citation_properties},
+  {Div = add_cito},
+}

example/paper.md

@@ -34,7 +34,7 @@ tags:
 # Summary
 
 This article describes the features of the Journal of Open Source
-Software [@smith2018] publishing pipeline. The publishing method
+Software [@usesMethodIn:smith2018] publishing pipeline. The publishing method
 is similar to the model described by @krewinkel2017, in that
 Markdown is used as the input format. The author-provided files
 serves as the source for all generated publishing artifacts.

scripts/entrypoint.sh

@@ -98,6 +98,7 @@ for format in $(printf "%s" "$outformats" | sed -e 's/,/ /g'); do
     # Note that the output file must be defined in the format's defaults file.
     /usr/local/bin/pandoc \
 	      --data-dir="$OPENJOURNALS_PATH"/data \
+        --lua-filter="$OPENJOURNALS_PATH"/data/filters/extract-cito.lua \
         --defaults=shared \
         --defaults="${format}" \
         --defaults="$OPENJOURNALS_PATH"/"${JOURNAL}"/defaults.yaml \