Use a Lua script for all transformations

inara.lua

@@ -0,0 +1,202 @@
+#!/usr/bin/env pandoc-lua
+
+PANDOC_VERSION:must_be_at_least {3,2}
+local arg = arg or {[0] = 'inara.lua'}
+local input_file = arg[1] or 'paper.md'
+
+-- Imports
+local io = require 'io'
+local pandoc = require 'pandoc'
+local List = require 'pandoc.List'
+local mediabag = require 'pandoc.mediabag'
+local path = require 'pandoc.path'
+local system = require 'pandoc.system'
+local template = require 'pandoc.template'
+local utils = require 'pandoc.utils'
+-- Functions
+local run_lua_filter = utils.run_lua_filter
+local read = pandoc.read
+
+-- Base settings
+local input_format = 'markdown'
+local paper_directory = path.directory(input_file)
+local output_directory =
+  path.normalize(
+    path.join {
+      system.get_working_directory(),
+      paper_directory
+    }
+  )
+
+local data_dir =
+  path.normalize(
+    path.join {
+      system.get_working_directory(),
+      path.directory(arg[0]),
+      'data'
+    }
+  )
+
+local function read_file (filename)
+  local fh = io.open(filename, 'r')
+  local contents = fh:read 'a'
+  fh:close()
+  return contents
+end
+
+local fh = io.open(input_file)
+local doc = read(fh:read 'a', input_format)
+fh:close()
+doc = system.with_working_directory(
+  paper_directory,
+  function () return mediabag.fill(doc) end
+)
+
+-- Set some specific metadata
+doc.meta.lang = 'en-US'  -- articles must be written in American English
+doc.meta['footer-csl'] = 'footer.csl'
+
+local shared_filters = List {
+  'parse-latex.lua',
+  'inline-cited-references.lua',
+  'normalize-metadata.lua',
+  'time.lua',
+  'normalize-author-names.lua',
+  'substitute-in-format.lua',
+}
+
+local formats = {
+  jats = {
+    format = 'jats_publishing',
+    filters = List {
+      'resolve-references.lua',
+      'remove-references-heading.lua',
+      'orcid-uri.lua',
+    },
+  },
+  pdf = {
+    format = 'latex',
+    filters = List{
+      'draft.lua',
+      'self-citation.lua',
+    },
+    write_output = function (tex, outfile)
+      system.with_temporary_directory(
+        'inara-pdf',
+        function (dirname)
+          system.with_working_directory(dirname, function ()
+            mediabag.write(dirname)
+            local texfh = io.open(path.join{dirname, 'inara-paper.tex'}, 'w')
+            texfh:write(tex)
+            texfh:close()
+            os.execute 'latexmk -lualatex inara-paper.tex'
+            local pdffile = path.join{dirname, 'inara-paper.pdf'}
+            local fh = io.open(outfile, 'w')
+            fh:write(io.open(pdffile):read'a')
+            fh:close()
+          end)
+        end
+      )
+    end
+  },
+}
+
+local function get_template (conf)
+  return conf.template
+    and io.open(path.join{data_dir, conf.template}):read 'a'
+    or template.default(conf.format)
+end
+
+-- FIXME!!
+local journal_metadata = {
+  ['csl'] = 'apa.csl',
+  ['joss_resource_url'] = 'N/A',
+  ['journal'] = {
+    ['abbrev-title'] = 'JOSS',
+    ['alias'] = 'joss',
+    ['url'] = 'https://joss.theoj.org',
+    ['doi'] = '10.21105/joss',
+    ['title'] = 'Journal of Open Source Software',
+    ['publisher-name'] = 'Open Journals',
+    ['issn'] = '2475-9066',
+    ['eissn'] = '2475-9066',
+  },
+  ['link-citations'] = true,
+  ['copyright'] = {
+    ['statement'] =
+      "Authors of papers retain copyright and release the work under a" ..
+      "Creative Commons Attribution 4.0 International License (CC BY 4.0)",
+    ['holder'] = 'The article authors',
+    ['year'] = '2024',
+    ['type'] = 'open-access',
+    ['link'] = 'https://creativecommons.org/licenses/by/4.0/',
+    ['text'] =
+      "Authors of papers retain copyright and release the work under a" ..
+      "Creative Commons Attribution 4.0 International License (CC BY 4.0)"
+  },
+  ['aas_logo_path'] = 'joss/aas-logo.png',
+  ['europar_logo_path'] = 'joss/europar-logo.png',
+  ['logo_path'] = 'joss/logo.png',
+}
+for key, value in pairs(journal_metadata) do
+  doc.meta[key] = value
+end
+local default_article_info = {
+  ['archive_doi'] = 'DOI unavailable',
+  ['editor_url'] = 'https://example.com',
+  ['repository'] = 'NO_REPOSITORY',
+  ['review_issue_url'] = 'N/A',
+  ['citation_author'] = '¿citation_author?',
+  ['editor_name'] = 'Pending Editor',
+  ['issue'] = '¿ISSUE?',
+  ['page'] = '¿PAGE?',
+  ['published_at'] = '1970-01-01',
+  ['reviewers'] = List{'Pending Reviewers'},
+  ['submitted_at'] = '1970-01-01',
+  ['volume'] = '¿VOL?',
+  ['doi_batch_id'] = 'N/A',
+  ['formatted_doi'] = 'DOI unavailable',
+  ['paper_url'] = 'NO PAPER URL',
+  ['draft'] = true,
+}
+for key, value in pairs(default_article_info) do
+  doc.meta[key] = value
+end
+doc.meta['footer-csl'] = io.open(path.join{data_dir, 'resources', 'footer.csl'})
+
+local target_formats = List {'jats', 'pdf'}
+
+local doc_orig = doc:clone()
+for _, format in ipairs(target_formats) do
+  doc = doc_orig:clone()
+  local format_conf = assert(formats[format], 'Unsupported format: ' .. format)
+  local output_format = format_conf.format
+  FORMAT = output_format
+  system.with_working_directory(
+    paper_directory,
+    function ()
+      for _, filter_name in ipairs(shared_filters) do
+        local filter_path = path.join{data_dir, 'filters', filter_name}
+        PANDOC_SCRIPT_FILE = filter_path
+        doc = run_lua_filter(doc, filter_path)
+      end
+
+      for _, filter_name in ipairs(format_conf.filters) do
+        local filter_path = path.join{data_dir, 'filters', filter_name}
+        PANDOC_SCRIPT_FILE = filter_path
+        doc = run_lua_filter(doc, filter_path)
+      end
+    end
+  )
+
+  -- Writer options
+  local wopts = {
+    template = get_template(format_conf),
+  }
+  local out = pandoc.write(doc, output_format, wopts)
+  if format_conf.write_output then
+    format_conf.write_output(out, path.join{output_directory, 'paper.pdf'})
+  else
+    print('Not writing', #out, 'characters')
+  end
+end