Use a Lua script for all transformations

Dockerfile

@@ -1,4 +1,4 @@
-FROM pandoc/latex:3.2.0-alpine
+FROM pandoc/latex:edge-alpine
 
 RUN apk add --no-cache ttf-hack
 
@@ -40,7 +40,7 @@ RUN TERM=dumb luaotfload-tool --update \
 ARG openjournals_path=/usr/local/share/openjournals
 COPY ./resources $openjournals_path
 COPY ./data $openjournals_path/data
-COPY ./scripts/entrypoint.sh /usr/local/bin/inara
+COPY ./inara.lua /usr/local/bin/inara
 
 ENV JOURNAL=joss
 ENV OPENJOURNALS_PATH=$openjournals_path

inara.lua

@@ -0,0 +1,357 @@
+#!/usr/bin/env pandoc-lua
+
+PANDOC_VERSION:must_be_at_least {3,2}
+local arg = arg or {[0] = 'inara.lua'}
+
+-- 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 sha1 = utils.sha1
+local run_lua_filter = utils.run_lua_filter
+local read = pandoc.read
+
+local usage = table.concat {
+  'Usage: %s [OPTIONS] INPUT_FILE\n',
+  'Options:\n',
+  '\t-l: create log files for all formats\n',
+  '\t-m: article info file; YAML file contains article metadata\n',
+  '\t-o: comma-separated list of output format; defaults to jats,pdf\n',
+  '\t-p: flag to force the production of a publishing PDF\n',
+  '\t-r: flag to produce a retraction-notice publishing PDF\n',
+  '\t-v: increase verbosity; can be given multiple times\n',
+}
+
+-- script options
+local options = {
+  verbosity = 0,
+  outformats = {'jats','pdf'},
+  retraction = false,
+  log = false,
+  article_info_file = nil,
+  draft = true,
+}
+local positional_args = List{}
+
+do
+  local i = 1
+  while i <= #arg do
+    if arg[i] == '-l' then
+      options.log = true
+      i = i + 1
+    elseif arg[i] == '-m' then
+      options.article_info_file = arg[i+1]
+      i = i + 2
+    elseif arg[i] == '-o' then
+      options.outformats = List{}
+      for f in arg[i+1]:gmatch '[^,]+' do
+        options.outformats:insert(f)
+      end
+      i = i + 2
+    elseif arg[i] == '-r' then
+      options.retraction = true
+      i = i + 1
+    elseif arg[i] == '-p' then
+      options.draft = false
+      i = i + 1
+    elseif arg[i] == '-m' then
+      options.verbosity = options.verbosity + 1
+      i = i + 1
+    elseif arg[i]:match '^%-' then
+      io.stderr:write(usage)
+    else
+      positional_args:insert(arg[i])
+      i = i + 1
+    end
+  end
+end
+
+local function ensure_absolute (filepath)
+  return path.normalize(
+    path.is_absolute(filepath)
+    and filepath
+    or path.join {system.get_working_directory(), filepath}
+  )
+end
+
+local input_file = positional_args[1] or 'paper.md'
+
+-- Base settings
+local input_format = 'markdown'
+local paper_directory = path.directory(input_file)
+local output_directory = ensure_absolute(paper_directory)
+
+local data_dir = path.join {
+  os.getenv 'OPENJOURNALS_PATH' or ensure_absolute(path.directory(arg[0])),
+  'data'
+}
+
+local resources_path = os.getenv 'OPENJOURNALS_PATH'
+  or path.join {ensure_absolute(path.directory(arg[0])), 'resources'}
+
+-- FIXME!!
+local journal_metadata = {
+  ['csl'] = 'apa.csl',
+  ['joss'] = true,
+  ['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'] = path.join{resources_path, 'joss/aas-logo.png'},
+  ['europar_logo_path'] = path.join{resources_path, 'joss/europar-logo.png'},
+  ['logo_path'] = path.join{resources_path, 'joss/logo.png'},
+}
+--
+-- File helpers
+--
+
+local function read_file (filename)
+  local fh = assert(io.open(filename, 'r'), "Couldn't open " .. filename)
+  local contents = fh:read 'a'
+  fh:close()
+  return contents
+end
+
+local function write_file (filename, contents)
+  if options.verbosity >= 0 then
+    io.stderr:write('Writing file ' .. filename .. '\n')
+  end
+  local fh = io.open(filename, 'wb')
+  fh:write(contents)
+  fh:close()
+end
+
+
+--- Map from old image filepaths to new names.
+local updated_filepath = {}
+
+local function unnest (filepath, contents)
+  if updated_filepath[filepath] then
+    return updated_filepath
+  end
+
+  local newpath = path.filename(filepath)
+  if updated_filepath[newpath] then
+    -- the filename is already in use. Prefix with sha1 hash.
+    newpath = sha1(contents) .. '-' .. filepath
+  end
+  updated_filepath[filepath] = newpath
+  return newpath
+end
+
+local function unnest_images (doc)
+  local newpath
+  for fp, mt, contents in mediabag.items() do
+    -- Delete all mediabag items and re-insert them under their fixed
+    -- name.
+    newpath = unnest(fp, contents)
+    mediabag.delete(fp)
+    mediabag.insert(newpath, mt, contents)
+  end
+  return doc:walk {
+    Image = function (img)
+      img.src = updated_filepath[img.src] or img.src
+      return img
+    end
+  }
+end
+
+--- Filters run for all formats
+local shared_filters = List {
+  'parse-latex.lua',
+  'inline-cited-references.lua',
+  utils.citeproc,
+  'normalize-metadata.lua',
+  'time.lua',
+  'normalize-author-names.lua',
+  'substitute-in-format.lua',
+}
+
+local formats = {
+  crossref = {
+    format = 'html5',
+    filters = List {
+      'doi-batch-id.lua',
+      'flatten-references.lua',
+    },
+    template = 'templates/default.crossref'
+  },
+  jats = {
+    format = 'jats_publishing',
+    extensions = {element_citations = true},
+    filters = List {
+      'resolve-references.lua',
+      'remove-references-heading.lua',
+      'orcid-uri.lua',
+      unnest_images,
+    },
+    outfile = function (_)
+      return path.join{'jats', 'paper.jats'}
+    end,
+    write_output = function (jats, outfile)
+      local outdir = outfile
+      outfile = path.join{outdir, 'paper.jats'}
+      system.make_directory(outdir, true)
+      write_file(outfile, jats)
+      pandoc.mediabag.write(outdir)
+      mediabag.write(outdir)
+    end
+  },
+  pdf = {
+    format = 'latex',
+    filters = List{
+      'draft.lua',
+      'self-citation.lua',
+      'fix-bibentry-spacing.lua',
+    },
+    reference_links = true,
+    template = 'templates/default.latex',
+    variables = {
+      -- styling options
+      colorlinks = true,
+      linkcolor = '[rgb]{0.0, 0.5, 1.0}',
+      urlcolor = '[rgb]{0.0, 0.5, 1.0}',
+    },
+    write_output = function (tex, outfile)
+      for _, key in ipairs{'logo_path', 'europar_logo_path', 'aas_logo_path'} do
+        local filepath = journal_metadata[key]
+        local content, mt = pandoc.mediabag.fetch(filepath)
+        pandoc.mediabag.insert(path, content, mt)
+      end
+      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
+
+local default_article_info = {
+  ['archive_doi'] = '10.5281',
+  ['citation_author'] = '¿citation_author?',
+  ['doi_batch_id'] = 'N/A',
+  ['draft'] = options.draft,
+  ['editor'] = {
+    name = 'Open Journals',
+    url = 'https://joss.theoj.org',
+    github_user = '@openjournals',
+  },
+  ['editor_name'] = 'Pending Editor',
+  ['editor_url'] = 'https://example.com',
+  ['formatted_doi'] = 'DOI unavailable',
+  ['issue'] = '¿ISSUE?',
+  ['page'] = '¿PAGE?',
+  ['paper_url'] = 'NO PAPER URL',
+  ['published_at'] = '1970-01-01',
+  ['repository'] = 'NO_REPOSITORY',
+  ['review_issue_url'] = 'N/A',
+  ['reviewers'] = List{'openjournals'},
+  ['software_repository_url'] = 'https://github.com/openjournals',
+  ['software_review_url'] = 'https://github.com/openjournals',
+  ['submitted_at'] = '1970-01-01',
+  ['volume'] = '¿VOL?',
+}
+
+local doc = read(read_file(input_file), input_format)
+doc = system.with_working_directory(
+  paper_directory,
+  function () return mediabag.fill(doc) end
+)
+for key, value in pairs(default_article_info) do
+  doc.meta[key] = value
+end
+for key, value in pairs(journal_metadata) do
+  doc.meta[key] = value
+end
+-- Set some specific metadata
+doc.meta.lang = 'en-US'  -- articles must be written in American English
+doc.meta['article-info-file'] = options.article_info_file and
+  ensure_absolute(options.article_info_file)
+doc.meta['footer-csl'] = path.join{resources_path, 'footer.csl'}
+doc.meta['csl'] = path.join{resources_path, 'apa.csl'}
+
+local doc_orig = doc:clone()
+for _, format in ipairs(options.outformats) do
+  io.stderr:write('Now converting to ' .. format .. '\n')
+  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 in ipairs(shared_filters .. format_conf.filters) do
+        if type(filter) == 'string' then
+          local filter_path = path.join{data_dir, 'filters', filter}
+          PANDOC_SCRIPT_FILE = filter_path
+          doc = run_lua_filter(doc, filter_path)
+        elseif type(filter) == 'function' then
+          doc = filter(doc)
+        else
+          error("Cannot handle filter of type " .. type(filter))
+        end
+      end
+    end
+  )
+
+  -- Writer options
+  local wopts = {
+    reference_links = format_conf.reference_links,
+    template = get_template(format_conf),
+    variables = format_conf.variables
+  }
+  local outstr = pandoc.write(doc, format_conf, wopts)
+  format_conf.outfile = format_conf.outfile
+    or function(_) return 'paper.' .. format end
+  local outfile = path.join{output_directory, format_conf.outfile(doc)}
+  if format_conf.write_output then
+    format_conf.write_output(outstr, outfile)
+  else
+    write_file(outfile, outstr)
+  end
+end