---------------------------------------------------------
----------------Auto generated code block----------------
---------------------------------------------------------
do
local searchers = package.searchers or package.loaders
local origin_seacher = searchers[2]
searchers[2] = function(path)
local files =
{
------------------------
-- Modules part begin --
------------------------
["prefix_ids_filter"] = function()
--------------------
-- Module: 'prefix_ids_filter'
--------------------
--- prefix_crossref_ids_filter, prefix_ids_filter: filters to prefix
-- sources's ids and links to avoid conflicts between sources.
-- These two filters will be ran on imported sources if we need to isolate
-- their internal crossreferences from other sources
-- The first filter, applied before the user's, handles Pandoc-crossref
-- crossreferences. The second, applied after, handles remaining
-- crossreferences.
return [[
---# Global variables
---@alias crossref.Prefixes 'fig'|'sec'|'eq'|'tbl'|'lst'
---@alias citeproc.Prefixes 'ref'
---@type string user's custom prefix
local prefix = ''
---@type pandoc.List identifers removed
local old_identifiers = pandoc.List:new()
---@type pandoc.List identifiers to ignore
local ids_to_ignore = pandoc.List:new()
---@type boolean whether to process pandoc-crossref links
local pandoc_crossref = true
---@type pandoc.List list of identifier prefixes for crossref
local crossref_prefixes = pandoc.List:new({'fig','sec','eq','tbl','lst'})
---@type pandoc.List list of identifier prefixes for citeproc
local citeproc_prefixes = pandoc.List:new({'ref'})
---@type pandoc.List list of identifier prefixes appearing in Str elements
local crossref_str_prefixes = pandoc.List:new({'eq','tbl','lst'})
---@type boolean whether pandoc-cross ref codeBlockCaptions option is on
local codeblock_captions = true
---type: pandoc-friendly type function
---pandoc.utils.type is only defined in Pandoc >= 2.17
---if it isn't, we extend Lua's type function to give the same values
---as pandoc.utils.type on Meta objects: Inlines, Inline, Blocks, Block,
---string and booleans
---Caution: not to be used on non-Meta Pandoc elements, the
---results will differ (only 'Block', 'Blocks', 'Inline', 'Inlines' in
--->=2.17, the .t string in <2.17).
local type = pandoc.utils.type or function (obj)
local tag = type(obj) == 'table' and obj.t and obj.t:gsub('^Meta', '')
return tag and tag ~= 'Map' and tag or type(obj)
end
---get_options: get filter options for document's metadata
---@param meta pandoc.Meta
---@return pandoc.Meta
function get_options(meta)
-- syntactic sugar: options aliases
-- merging behaviour: aliases prevail
local aliases = {'prefix', 'pandoc-crossref'}
for _,alias in ipairs(aliases) do
if meta['prefix-ids-' .. alias] ~= nil then
-- create a 'prefix-ids' key if needed
if not meta['prefix-ids'] then
meta['prefix-ids'] = pandoc.MetaMap({})
end
meta['prefix-ids'][alias] = meta['prefix-ids-' .. alias]
meta['prefix-ids-' .. alias] = nil
end
end
-- save options in global variables
if meta['prefix-ids'] then
if meta['prefix-ids']['prefix'] then
prefix = pandoc.utils.stringify(meta['prefix-ids']['prefix'])
end
if meta['prefix-ids']['pandoc-crossref'] ~= nil
and meta['prefix-ids']['pandoc-crossref'] == false then
pandoc_crossref = false
end
if meta['prefix-ids'].ignoreids and
type(meta['prefix-ids'].ignoreids) == 'List' then
ids_to_ignore:extend(meta['prefix-ids'].ignoreids)
end
end
-- pandoc-crossref option: meta.codeBlockCaptions
-- if meta.codeBlockCaptions is false then we should *not*
-- process `lst:label` identifiers that appear in Str elements
-- (that is, in codeblock captions). We will still convert
-- those that appear as CodeBlock attributes
if not meta.codeBlockCaptions then
codeblock_captions = false
crossref_str_prefixes = crossref_str_prefixes:filter(
function(item) return item ~= 'lst' end)
end
return meta
end
---process_doc: process the pandoc document.
---generates a prefix if needed, walks through the document
---and adds a prefix to all elements with identifier.
---@TODO meta fields may contain identifiers? abstract, thanks
---@param doc pandoc.Doc
---@return pandoc.Doc
function process_doc(doc)
-- add_prefix function
-- adds prefix to an identifier
-- do not add prefixes to empty identifiers
-- store the old identifiers in order to fix links
add_prefix = function (el)
if el.identifier and el.identifier ~= ''
and not ids_to_ignore:find(el.identifier) then
-- if citeproc type, add the prefix after "ref-"
local type, identifier = el.identifier:match('^(%a+)%-(.*)')
if type and identifier and citeproc_prefixes:find(type) then
old_identifiers:insert(el.identifier)
el.identifier = type..'-'..prefix..identifier
return el
end
-- if pandoc-crossref type, we add the prefix after "fig:", "tbl:", ...
-- though (like pandoc-crossref) we must ignore #lst:label unless there's
-- a caption attribute or the codeblock caption syntax is on
if pandoc_crossref then
local type, identifier = el.identifier:match('^(%a+):(.*)')
if type and identifier and crossref_prefixes:find(type) then
-- special case in which we don't touch it:
-- a codeblock with #lst:label id but no caption
-- nor caption table syntax on
if el.t == 'CodeBlock' and not codeblock_captions
and type == 'lst' and (not el.attributes
or not el.attributes.caption) then
return
-- in all other cases we add prefix between `type`
-- and `identifier`
-- NOTE: in principle we should check that if it's
-- a codeblock it has a caption paragraph before or
-- after, but that requires going through the doc
-- el by el, not worth it.
else
old_identifiers:insert(el.identifier)
el.identifier = type..':'..prefix..identifier
return el
end
end
end
-- if no pandoc_crossref action was taken, apply simple prefix
old_identifiers:insert(el.identifier)
el.identifier = prefix .. el.identifier
return el
end
end
-- add_prefix_string function
-- same as add_prefix but for pandoc-crossref "{eq:label}" strings
-- crossref_srt_prefixes tell us which ones to convert
add_prefix_string = function(el)
local type, identifier = el.text:match('^{#(%a+):(.*)}')
if type and identifier
and crossref_str_prefixes:find(type)
and not ids_to_ignore:find(type .. ':' .. identifier) then
old_identifiers:insert(type .. ':' .. identifier)
local new_id = type .. ':' .. prefix .. identifier
return pandoc.Str('{#' .. new_id .. '}')
end
end
-- process_identifiers function
-- apply the add_prefix and add_prefix_strings functions to blocks
process_identifiers = function(blocks)
local div = pandoc.walk_block(pandoc.Div(blocks), {
Span = add_prefix,
Link = add_prefix,
Image = add_prefix,
Code = add_prefix,
Div = add_prefix,
Header = add_prefix,
Table = add_prefix,
CodeBlock = add_prefix,
Str = pandoc_crossref and add_prefix_string
})
return div.content
end
-- function to add prefixes to links
local add_prefix_to_link = function (link)
if link.target:sub(1,1) == '#'
and old_identifiers:find(link.target:sub(2,-1)) then
local target = link.target:sub(2,-1)
-- handle citeproc targets
local type, identifier = target:match('^(%a+)%-(.*)')
if type and identifier and citeproc_prefixes:find(type) then
target = '#'..type..'-'..prefix..identifier
-- handle pandoc-crossref types targets if needed
elseif pandoc_crossref then
local type, identifier = target:match('^(%a+):(.*)')
if type and crossref_prefixes:find(type) then
target = '#' .. type .. ':' .. prefix .. identifier
else
target = '#' .. prefix .. target
end
else
target = '#' .. prefix .. target
end
link.target = target
return link
end
end
-- function to add prefixes to pandoc-crossref citations
-- looking for keys starting with `fig:`, `sec:`, `eq:`, ...
add_prefix_to_crossref_cites = function (cite)
for i = 1, #cite.citations do
local type, identifier = cite.citations[i].id:match('^(%a+):(.*)')
if type and identifier and crossref_prefixes:find(type) then
-- put the type in lowercase to match Fig: and fig:
-- note that sec: cites might refer to an old identifier
-- that doesn't start with sec:
local stype = pandoc.text.lower(type)
if old_identifiers:find(stype..':'..identifier) or
(stype == 'sec' and old_identifiers:find(identifier))
then
cite.citations[i].id = type..':'..prefix..identifier
end
end
end
return cite
end
-- function to process links and cites in some blocks
local process_links = function(blocks)
local div = pandoc.walk_block(pandoc.Div(blocks), {
Link = add_prefix_to_link,
Cite = pandoc_crossref and add_prefix_to_crossref_cites
})
return div.content
end
-- MAIN BODY
-- generate prefix if needed
if prefix == '' then
prefix = pandoc.utils.sha1(pandoc.utils.stringify(doc.blocks))
end
-- prefix identifiers in doc and in metadata fields with blocks content
for key,val in pairs(doc.meta) do
if type(val) == 'Blocks' then
doc.meta[key] = pandoc.MetaBlocks(
process_identifiers(pandoc.List(val))
)
elseif type(val) == 'List' then
for i = 1, #val do
if type(val[i]) == 'Blocks' then
doc.meta[key][i] = pandoc.MetaBlocks(
process_identifiers(pandoc.List(val[i]))
)
end
end
end
end
doc.blocks = process_identifiers(doc.blocks)
-- process links and cites in metadata fields and in body
for key,val in pairs(doc.meta) do
if type(val) == 'Blocks' then
doc.meta[key] = pandoc.MetaBlocks(
process_links(pandoc.List(val))
)
elseif type(val) == 'List' then
for i = 1, #val do
if type(val[i]) == 'Blocks' then
doc.meta[key][i] = pandoc.MetaBlocks(
process_links(pandoc.List(val[i]))
)
end
end
end
end
doc.blocks = process_links(doc.blocks)
-- return the result
return doc
end
-- # Main filter
return {
{
Meta = get_options,
Pandoc = process_doc
}
}
]]
end,
["file"] = function()
--------------------
-- Module: 'file'
--------------------
local system = pandoc.system
local path = pandoc.path
-- ## File module
local file = {}
---Whether a file exists
---@param filepath string
---@return boolean
function file.exists(filepath)
local f = io.open(filepath, 'r')
if f ~= nil then
io.close(f)
return true
else
return false
end
end
---read file as string (default) or binary.
---@param filepath string file path
---@param mode? 'b'|'t' 'b' for binary or 't' for text (default text)
---@return boolean success
---@return string? contents file contents if success
function file.read(filepath, mode)
local mode = mode == 'b' and 'rb' or 'r'
local contents
local f = io.open(filepath, mode)
if f then
contents = f:read('a')
f:close()
return true, contents
else
return false
end
end
---Write string to file in text or binary mode.
---@param contents string file contents
---@param filepath string file path
---@param mode? 'b'|'t' 'b' for binary or 't' for text (default text)
---@return boolean success
function file.write(contents, filepath, mode)
local mode = mode == 'b' and 'wb' or 'w'
local f = io.open(filepath, mode)
if f then
f:write(contents)
f:close()
return true
else
return false
end
end
return file
end,
["prefix_crossref_ids_filter"] = function()
--------------------
-- Module: 'prefix_crossref_ids_filter'
--------------------
--- prefix_crossref_ids_filter, prefix_ids_filter: filters to prefix
-- sources's ids and links to avoid conflicts between sources.
-- These two filters will be ran on imported sources if we need to isolate
-- their internal crossreferences from other sources
-- The first filter, applied before the user's, handles Pandoc-crossref
-- crossreferences. The second, applied after, handles remaining
-- crossreferences.
return [[
-- # Global variables
---@type string user's custom prefix
local prefix = ''
---@type pandoc.List identifers removed
local old_identifiers = pandoc.List:new()
---@type pandoc.List identifers added
local new_identifiers = pandoc.List:new()
---@type pandoc.List identifiers to ignore
local ids_to_ignore = pandoc.List:new()
---@type boolean whether to process pandoc-crossref links
local pandoc_crossref = true
local crossref_prefixes = pandoc.List:new({'fig','sec','eq','tbl','lst',
'Fig','Sec','Eq','Tbl','Lst'})
local crossref_str_prefixes = pandoc.List:new({'eq','tbl','lst',
'Eq','Tbl','Lst'}) -- found in Str elements (captions or after eq)
local codeblock_captions = true -- is the codeblock caption syntax on?
--- type: pandoc-friendly type function
-- pandoc.utils.type is only defined in Pandoc >= 2.17
-- if it isn't, we extend Lua's type function to give the same values
-- as pandoc.utils.type on Meta objects: Inlines, Inline, Blocks, Block,
-- string and booleans
-- Caution: not to be used on non-Meta Pandoc elements, the
-- results will differ (only 'Block', 'Blocks', 'Inline', 'Inlines' in
-- >=2.17, the .t string in <2.17).
local type = pandoc.utils.type or function (obj)
local tag = type(obj) == 'table' and obj.t and obj.t:gsub('^Meta', '')
return tag and tag ~= 'Map' and tag or type(obj)
end
--- get_options: get filter options for document's metadata
-- @param meta pandoc Meta element
function get_options(meta)
-- syntactic sugar: options aliases
-- merging behaviour: aliases prevail
local aliases = {'prefix', 'pandoc-crossref'}
for _,alias in ipairs(aliases) do
if meta['prefix-ids-' .. alias] ~= nil then
-- create a 'prefix-ids' key if needed
if not meta['prefix-ids'] then
meta['prefix-ids'] = pandoc.MetaMap({})
end
meta['prefix-ids'][alias] = meta['prefix-ids-' .. alias]
meta['prefix-ids-' .. alias] = nil
end
end
-- save options in global variables
if meta['prefix-ids'] then
if meta['prefix-ids']['prefix'] then
prefix = pandoc.utils.stringify(meta['prefix-ids']['prefix'])
end
if meta['prefix-ids']['pandoc-crossref'] ~= nil
and meta['prefix-ids']['pandoc-crossref'] == false then
pandoc_crossref = false
end
end
-- if meta.codeBlockCaptions is false then we should *not*
-- process `lst:label` identifiers that appear in Str elements
-- (that is, in codeblock captions). We will still convert
-- those that appear as CodeBlock attributes
if not meta.codeBlockCaptions then
codeblock_captions = false
crossref_str_prefixes = crossref_str_prefixes:filter(
function(item) return item ~= 'lst' end)
end
return meta
end
--- process_doc: process the pandoc document
-- generates a prefix if needed, walk through the document
-- and adds a prefix to all elements with identifier.
-- @param pandoc Pandoc element
-- @TODO handle meta fields that may contain identifiers? abstract
-- and thanks?
function process_doc(doc)
-- generate prefix if needed
if prefix == '' then
prefix = pandoc.utils.sha1(pandoc.utils.stringify(doc.blocks))
end
-- add_prefix function
-- check that it's a pandoc-crossref type
-- do not add prefixes to empty identifiers
-- store the old identifiers to later fix links
add_prefix = function (el)
if el.identifier and el.identifier ~= '' then
-- if pandoc-crossref type, we add the prefix after "fig:", "tbl", ...
-- though (like pandoc-crossref) we must ignore #lst:label unless there's
-- a caption attribute or the codeblock caption syntax is on
if pandoc_crossref then
local type, identifier = el.identifier:match('^(%a+):(.*)')
if type and identifier and crossref_prefixes:find(type) then
-- special case in which we don't touch it:
-- a codeblock with #lst:label id but no caption
-- nor caption table syntax on
if el.t == 'CodeBlock' and not codeblock_captions
and type == 'lst' and (not el.attributes
or not el.attributes.caption) then
return
-- in all other cases we add prefix between `type`
-- and `identifier`
-- NOTE: in principle we should check that if it's
-- a codeblock it has a caption paragraph before or
-- after, but that requires going through the doc
-- el by el, not worth it.
else
old_identifiers:insert(type .. ':' .. identifier)
new_id = type .. ':' .. prefix .. identifier
el.identifier = new_id
new_identifiers:insert(new_id)
return el
end
end
end
-- if no pandoc_crossref action was taken, apply simple prefix
-- Warning: if `autoSectionLabels` is true, pandoc-crossref
-- will add `sec:` to Header element ids; so we anticipate that
old_identifiers:insert(el.identifier)
new_id = prefix .. el.identifier
el.identifier = new_id
if el.t == 'Header'
and doc.meta.autoSectionLabels ~= false then
new_identifiers:insert('sec:' .. new_id)
else
new_identifiers:insert(new_id)
end
return el
end
end
-- add_prefix_string function
-- handles {#eq:label} for equations and {#tbl:label} or {#lst:label}
-- in table or listing captions.
add_prefix_string = function(el)
local type, identifier = el.text:match('^{#(%a+):(.*)}')
if type and identifier and crossref_str_prefixes:find(type) then
old_identifiers:insert(type .. ':' .. identifier)
local new_id = type .. ':' .. prefix .. identifier
new_identifiers:insert(new_id)
return pandoc.Str('{#' .. new_id .. '}')
end
end
-- process_identifiers function
-- apply the add_prefix and add_prefix_strings functions to
-- elements with pandoc-crossref identifiers
process_identifiers = function(blocks)
local div = pandoc.walk_block(pandoc.Div(blocks), {
CodeBlock = add_prefix,
Figure = add_prefix,
Header = add_prefix,
Table = add_prefix,
Code = add_prefix,
Image = add_prefix,
--Link = add_prefix, REMOVED css writers might not expect it
Str = add_prefix_string,
})
return div.content
end
-- prefix identifiers in doc and in metadata fields with blocks content
for key,val in pairs(doc.meta) do
if type(val) == 'Blocks' then
doc.meta[key] = pandoc.MetaBlocks(
process_identifiers(pandoc.List(val))
)
elseif type(val) == 'List' then
for i = 1, #val do
if type(val[i]) == 'Blocks' then
doc.meta[key][i] = pandoc.MetaBlocks(
process_identifiers(pandoc.List(val[i]))
)
end
end
end
end
doc.blocks = process_identifiers(doc.blocks)
-- function to add prefixes to links
local add_prefix_to_link = function (link)
if link.target:sub(1,1) == '#'
and old_identifiers:find(link.target:sub(2,-1)) then
local target = link.target:sub(2,-1)
local type = target:match('^(%a+):')
if crossref_prefixes:find(type) then
link.target = '#' .. type .. ':' .. prefix
.. target:match('^%a+:(.*)')
return link
end
end
end
-- function to add prefixes to pandoc-crossref citations
-- looking for keys starting with `fig:`, `sec:`, `eq:`, ...
local add_prefix_to_crossref_cites = function (cite)
for i = 1, #cite.citations do
local type, identifier = cite.citations[i].id:match('^(%a+):(.*)')
if type and identifier and crossref_prefixes:find(type) then
-- put the type in lowercase to match Fig: and fig:
-- note that sec: cites might refer to an old identifier
-- that doesn't start with sec:
local stype = pandoc.text.lower(type)
if old_identifiers:find(stype..':'..identifier) or
(stype == 'sec' and old_identifiers:find(identifier))
then
cite.citations[i].id = type..':'..prefix..identifier
end
end
end
return cite
end
-- function to process links and cites in some blocks
process_links = function(blocks)
local div = pandoc.walk_block(pandoc.Div(blocks), {
Link = add_prefix_to_link,
Cite = pandoc_crossref and add_prefix_to_crossref_cites
})
return div.content
end
-- process links and cites in doc and in metablocks fields
for key,val in pairs(doc.meta) do
if type(val) == 'Blocks' then
doc.meta[key] = pandoc.MetaBlocks(
process_links(pandoc.List(val))
)
elseif type(val) == 'List' then
for i = 1, #val do
if type(val[i]) == 'Blocks' then
doc.meta[key][i] = pandoc.MetaBlocks(
process_links(pandoc.List(val[i]))
)
end
end
end
end
doc.blocks = process_links(doc.blocks)
-- set metadata (in case prefix-ids is ran later on)
-- save a list of ids changed
if not doc.meta['prefix-ids'] then
doc.meta['prefix-ids'] = pandoc.MetaMap({})
end
doc.meta['prefix-ids'].ignoreids = pandoc.MetaList(new_identifiers)
-- return the result
return doc
end
-- # Main filter
return {
{
Meta = get_options,
Pandoc = function(doc)
if pandoc_crossref then return process_doc(doc) end
end,
}
}
]]
end,
["normalize_meta"] = function()
--------------------
-- Module: 'normalize_meta'
--------------------
--[[
normalize_meta
Normalize metadata options for collection
]]
local log = require('log')
local type = pandoc.utils.type
local stringify = pandoc.utils.stringify
--- syntactic_sugar: normalize alias keys in meta
-- in case of duplicates we warn the user and
-- use the ones with more explicit names.
-- if `collection` or `offprints` are strings
-- we assume they're defaults filepaths.
local function normalize_meta(meta)
-- function that converts aliases to official fields in a map
-- following an alias table.
-- The map could be the doc's Meta or a MetaMap within it.
-- Use `root` to let the user know what the root key was in the
-- later case in error messages, e.g. "imports[1]/".
-- Merging behaviour: if the official already exists we warn the
-- user and simply ignore the alias key.
-- Warning: aliases must be acceptable Lua map keys, so they can't
-- contain e.g. dashes. Official names aren't restricted.
-- @alias_table table an alias map aliasname = officialname.
-- @root string names the root for error messages, e.g. "imports[1]/"
-- @map Meta or MetaMap to be cleaned up
function make_official(alias_table, root, map)
if type(map) == 'table' or type(map) == 'Meta' then
for alias,official in pairs(alias_table) do
if map[alias] and map[official] then
log('WARNING', 'Metadata: `'..root..alias..'` '
..'is a duplicate of `'..root..official..'`, '
..'it will be ignored.')
map[alias] = nil
elseif map[alias] then
map[official] = map[alias]
map[alias] = nil
end
end
end
return map
end
local aliases = {
global = 'global-metadata',
metadata = 'child-metadata',
}
meta = make_official(aliases, '', meta)
if meta.imports and type(meta.imports) == 'List' then
local aliases = {
metadata = 'child-metadata'
}
for i = 1, #meta.imports do
local rt = 'imports[' .. i .. ']/'
meta.imports[i] = make_official(aliases, rt, meta.imports[i])
end
end
if meta.collection and type(meta.collection) ~= 'table' then
local filepath = stringify(meta.collection)
log('INFO', 'Assuming `collection` is a defaults file '
.. 'filepath: ' .. filepath .. '.' )
meta.collection = pandoc.MetaMap({
defaults = filepath
})
end
if meta.offprints and type(meta.offprints) ~= 'table' then
local filepath = stringify(meta.offprints)
log('INFO', 'Assuming `offprints` is a defaults file '
.. 'filepath: ' .. filepath .. '.' )
meta.offprints = pandoc.MetaMap({
defaults = filepath
})
end
return meta
end
return normalize_meta
end,
["log"] = function()
--------------------
-- Module: 'log'
--------------------
local FILTER_NAME = 'Recursive-Citeproc'
---log: send message to std_error
---@param type 'INFO'|'WARNING'|'ERROR'
---@param text string error message
local function log(type, text)
local level = {INFO = 0, WARNING = 1, ERROR = 2}
if level[type] == nil then type = 'ERROR' end
if level[PANDOC_STATE.verbosity] <= level[type] then
local message = '[' .. type .. '] '..FILTER_NAME..': '.. text .. '\n'
io.stderr:write(message)
end
end
return log
end,
----------------------
-- Modules part end --
----------------------
}
if files[path] then
return files[path]
else
return origin_seacher(path)
end
end
end
---------------------------------------------------------
----------------Auto generated code block----------------
---------------------------------------------------------
--[[-- # Collection builder - Building collections with Pandoc
@author Julien Dutant <https://github.com/jdutant>
@copyright 2021-2024 Philosophie.ch
@license MIT - see LICENSE file for details.
@release 0.5
]]
PANDOC_VERSION:must_be_at_least '3.1.1' -- for pandoc.json
local system = pandoc.system
local path = pandoc.path
local stringify = pandoc.utils.stringify
local type = pandoc.utils.type
local log = require('log')
local file = require('file')
local prefix_crossref_ids_filter = require('prefix_crossref_ids_filter')
local prefix_ids_filter = require('prefix_ids_filter')
local normalize_meta = require('normalize_meta')
-- # Filter settings
-- environement variables
local env = {
working_directory = system.get_working_directory(),
}
env.input_folder = path.directory(PANDOC_STATE['input_files'][1])
-- setup map
-- further fields that may be added:
-- - gather: strings list, metadata keys to gather from children
-- - replace: strings list, metadata keys to be replaced by children's ones
-- - pass: strings list, metadata keys to be passed onto children
-- - globalize: strings list, metadata keys to be made global onto children
local setup = {
do_something = false, -- whether the filter needs to do anything
isolate = false, -- whether to isolate sources by default
needs_isolate_filter = false, -- whether the prefix-ids filters are needed
offprint_mode = false, -- whether we're in offprint mode
}
-- # Helper functions
--- meta_to_yaml: converts MetaMap to yaml, returns empty string if failed.
---@param map pandoc.MetaMap
---@return string result
local function meta_to_yaml (map)
if type(map) ~= 'Meta' then
map = pandoc.Meta(map)
end
---@param str string
---@return string
local function extract_yaml (str)
return str:match("^%-%-%-\n(.*\n)%-%-%-\n") or ''
end
local str = pandoc.write(
pandoc.Pandoc({}, map),
'markdown',
{template = pandoc.template.default('markdown')}
)
return extract_yaml(str)
end
---save Meta or Metamap as a yaml file
-- uses pandoc to convert Meta or Metamap to yaml.
-- a converter would be faster, but would need to parse Meta elements.
---comment
---@param map pandoc.Meta|pandoc.MetaMap
---@param filepath string
---@return boolean success
local function save_meta_as_yaml(map, filepath)
yaml = meta_to_yaml(map)
local success = file.write(yaml, filepath)
if success then
return true
else
return false
end
end
-- # Collection functions
--- gather_and_replace: gather or replace selected keys in the main
-- document based on source files metadata.
-- Keys to be gather or replaced are listed in `setup.gather` and
-- `setup.replace`.
-- Gather behaviour: if a key preexists we make a list with the old and
-- new values; it both are lists we merge them. Useful for bibliographies,
-- header-includes.
-- Replace behaviour: if a key preexists we replace it with the source's
-- values; if present in different sources, the last one prevails. Useful
-- in offprint mode (single source) or for keys that don't overlap across
-- sources.
-- If a key is set to be gathered and replaced, it will be replaced.
local function gather_and_replace(meta)
for _,item in ipairs(meta.imports) do
-- we know `item `is a MetaMap, but not if it has a `file` key
-- if it doesn't we skip it
if not item.file then
goto continue
end
-- read and parse the file
local filepath = stringify(item.file)
local success, contents = file.read(filepath)
if not success then
log('ERROR', 'Cannot read file '..filepath..'.')
return
end
local itemdoc = pandoc.read(contents)
-- for each key to gather, we check if it exists
-- and we import it in our document's metadata
-- merging behaviour:
-- if the preexisting is a list, we append
-- if the preexisting key has a value, we turn into
-- a list and we append
if setup.gather then
for _,key in ipairs(setup.gather) do
if itemdoc.meta[key] then
if not meta[key] then
meta[key] = itemdoc.meta[key]:clone()
else
if type(meta[key]) ~= 'List' then
meta[key] = pandoc.MetaList(meta[key])
end
if type(itemdoc.meta[key]) == 'List' then
meta[key]:extend(itemdoc.meta[key])
else
meta[key]:insert(itemdoc.meta[key])
end
end
end
end
end
-- for each key to replace, we import it in the document's meta
if setup.replace then
for _,key in ipairs(setup.replace) do
if itemdoc.meta[key] then
meta[key] = itemdoc.meta[key]
end
end
end
:: continue ::
end
return meta
end
--- globalize_and_pass: globalize selected metadata fields into
-- the `global-metadata` map and place selected metadata fields into
-- the `child-metadata` map.
-- merging behaviour: warn and erase preexisting keys in `global/child
-- -metadata`.
-- creates `global/child-metadata` keys only if needed
-- @param meta
-- @param setup.globalize global variable
-- @return metadata document
local function globalize_and_pass(meta)
-- mapping `setup` keys with `meta` keys
local map = {
globalize = 'global-metadata',
pass = 'child-metadata'
}
for setupkey, metakey in pairs(map) do
-- are there `setup.globalize` or `setup.pass` keys?
if setup[setupkey] then
for _,key in ipairs(setup[setupkey]) do
-- is there a `key` field in metadata to copy?
if meta[key] then
-- copy in the `metakey` field, warn if merging
if not meta[metakey] then
meta[metakey] = pandoc.MetaMap({})
meta[metakey][key] = meta[key]
elseif not meta[metakey][key] then
meta[metakey][key] = meta[key]
else
-- "pass/globalize `key` replaced `key` in `metakey`"
log('WARNING', 'Metadata: ' .. setupkey ..
' `' .. key .. '` replaced `' .. key ..
'` in `' .. metakey .. '`.')
meta[metakey][key] = meta[key]
end
end
end
end
end
return meta
end
--- import_sources: import sources into the main document
-- passes metadata to sources using a temporary metadata file,
-- runs pandoc on them in the required mode and places the
-- result in the main document
local function import_sources(doc, tmpdir)
-- CONSTANTS
local acceptable_modes = pandoc.List:new({'native', 'raw', 'direct'})
-- save_yaml_if_needed: if element isn't a map, assume it's
-- a filepath to metadata file; otherwise save a temp
-- yaml file `default_filename`. Either way, returns a filepath.
local function save_yaml_if_needed(element, default_filename)
if type(element) ~= 'table' and type(element) ~= 'Meta' then
return stringify(element)
else
local filepath = path.join({tmpdir, default_filename})
local success = save_meta_as_yaml(element,filepath)
if not success then
log('ERROR', 'Could not write '..filepath..'.')
os.exit(1)
else
return filepath
end
end
end
-- GENERIC import features: metadata, defaults, mode, isolation
local generic_meta_fpath = ''
local generic_defaults_fpath = ''
local generic_mode = 'native'
-- Do we need to pass generic metadata?
-- If yes, prepare a temp file
if doc.meta['global-metadata'] or doc.meta['child-metadata'] then
generic_meta_fpath = path.join( { tmpdir , 'generic_meta.yaml' })
-- `child-metadata` goes to the root, `global-metadata` is
-- inserted as is
local metamap = pandoc.MetaMap(doc.meta['child-metadata'] or {})
metamap['global-metadata'] = doc.meta['global-metadata'] or nil
save_meta_as_yaml(metamap, generic_meta_fpath)
end
-- Do we need to pass generic defaults?
-- If yes, are we given a file or a map to save as a temp file?
-- (yes if `collection` has a `defaults` key that is a map)
if doc.meta.collection and doc.meta.collection.defaults then
generic_defaults_fpath = save_yaml_if_needed(
doc.meta.collection.defaults, 'generic_defaults.yaml')
end
-- DEBUG: display a temp yaml files
-- local file = io.open(generic_meta_fpath, 'r')
-- print('Generic meta yaml file ', generic_meta_fpath, ':')
-- print(file:read('a'))
-- file:close()
-- local file = io.open(generic_defaults_fpath, 'r')
-- print('Generic defaults yaml file ', generic_defaults_fpath, ':')
-- print(file:read('a'))
-- file:close()
-- set a generic import mode
if doc.meta.collection and doc.meta.collection['mode'] then
str = stringify(doc.meta.collection['mode'])
if acceptable_modes:find(str) then
generic_mode = str
end
end
-- will we need our internal filters?
-- if yes, save them as tmp files
-- for the isolate filter, get any user-specified custom prefix pattern
local isolate_prefix_pattern = "c%d-"
local prefix_ids_filter_fpath = ''
local prefix_crossref_ids_filter_fpath = ''
if setup.needs_isolate_filter then
if doc.meta.collection['isolate-prefix-pattern'] then
isolate_prefix_pattern = stringify(doc.meta.collection['isolate-prefix-pattern'])
end
prefix_ids_filter_fpath = path.join({tmpdir, 'prefix-ids.lua'})
prefix_crossref_ids_filter_fpath = path.join({tmpdir,
'prefix-crossref-ids.lua'})
local file = io.open(prefix_ids_filter_fpath, 'w')
file:write(prefix_ids_filter)
file:close()
local file = io.open(prefix_crossref_ids_filter_fpath, 'w')
file:write(prefix_crossref_ids_filter)
file:close()
end
-- MAIN LOOP to import each item in the list
-- `i` will be used as unique identifier if needed
for i = 1, #doc.meta.imports do
item = doc.meta.imports[i]
-- we can rely on item being a MetaMap
-- but if it doesn't have a `file` field nothing to do,
-- move on to the next one
if not item.file then
goto continue
end
-- LOCAL import features: source, metadata, defaults, mode, merge
local source = stringify(item.file)
local local_meta_fpath = ''
local local_defaults_fpath = ''
local mode = generic_mode
local merge_defaults = false
local merge_meta = true
local isolate = false
-- do we need local metadata?
if item['child-metadata'] then
local_meta_fpath = save_yaml_if_needed(
item['child-metadata'], 'local_meta.yaml' )
end
-- DEBUG: display local yaml file
-- if local_meta_fpath ~= '' then
-- print('IMPORT #', i, local_meta_fpath)
-- local f = io.open(local_meta_fpath, 'r')
-- print(f:read('a'))
-- f:close()
-- end
-- do we need local defaults?
if item['defaults'] then
local_defaults_fpath = save_yaml_if_needed(
item['defaults'], 'local_defaults.yaml' )
end
-- do we have a local mode?
if item.mode then
local str = stringify(item.mode)
if acceptable_modes:find(str) then
mode = str
end
end
-- merge meta and or defaults?
if item['merge-defaults'] and item['merge-defaults'] == true then
merge_defaults = true
end
if item['merge-metadata'] and item['merge-metadata'] == true then
merge_meta = true
end
-- isolate this specific item?
if item.isolate and item.isolate == true then
isolate = true
elseif item.isolate and item.isolate == false then
isolate = false
else
isolate = setup.isolate
end
-- COMMAND LINE ARGUMENTS
-- source filepath
local arguments = pandoc.List:new({source})
-- add source's directory to the resource path, if different
-- from the working directory.
-- in case biblios, defaults, are specified relative to it
-- get current resource path table, insert the source folder
if path.directory(source) ~= '.' then
local paths = pandoc.List:new(PANDOC_STATE.resource_path)
paths:insert(path.directory(source))
-- build a string with paths separated by ':'
local path_str = ''
for i = 1, #paths do
path_str = path_str .. paths[i]
if i < #paths then
path_str = path_str .. ':'
end
end
if path_str ~= '' then
arguments:extend({'--resource-path', path_str})
end
end
-- if isolate, add a prefix and apply the pandoc-crossref
-- filter upfront
if isolate then
arguments:extend({
'-M', 'prefix-ids-prefix=' ..
string.format(isolate_prefix_pattern, i),
'-L', prefix_crossref_ids_filter_fpath,
})
end
-- add any generic defaults and metadata
-- if no local ones provided or if we're asked to merge
if generic_meta_fpath ~= '' then
if local_meta_fpath == '' or merge_meta == true then
arguments:extend({'--metadata-file', generic_meta_fpath})
end
end
if generic_defaults_fpath ~= '' then
if local_defaults_fpath == '' or merge_defaults == true then
arguments:extend({'--defaults', generic_defaults_fpath})
end
end
-- add any local defaults and metadata
if local_meta_fpath ~= '' then
arguments:extend({'--metadata-file', local_meta_fpath})
end
if local_defaults_fpath ~= '' then
arguments:extend({'--defaults', local_defaults_fpath})
end
-- match verbosity
if PANDOC_STATE.verbosity == 'INFO' then
arguments:insert('--verbose')
elseif PANDOC_STATE.verbosity == 'ERROR' then
arguments:insert('--quiet')
end
-- if isolate, apply the prefix-ids filter last
if isolate then
arguments:extend({'-L', prefix_ids_filter_fpath})
end
-- function to inform users of the command we're running
local function inform(src, args)
local argstring = ''
for i = 2, #args do
argstring = argstring .. ' ' .. args[i]
end
log('INFO', 'Running pandoc on ' .. src .. ' with ' .. argstring)
end
-- run the commands for the required mode
if mode == 'native' then
-- @TODO need to modify to have FORMAT right and yet
-- catch the result in native format
-- @TODO piping may fail in windows WSL
arguments:extend({'-t', 'json'})
inform(source, arguments)
local result = pandoc.read(pandoc.pipe('pandoc', arguments, ''), 'json')
doc.blocks:extend(result.blocks)
elseif mode == 'raw' then
arguments:extend({'-t', FORMAT})
inform(source, arguments)
-- piping on Win (WSL) adds newlines. We save to a temp file instead
-- local result = pandoc.pipe('pandoc', arguments, '')
-- doc.blocks:insert(pandoc.RawBlock(FORMAT, result))
local tmp_outfile = path.join {tmpdir, 'out.'..FORMAT}
arguments:extend({'-o', tmp_outfile })
pandoc.pipe('pandoc', arguments, '')
local file = io.open(tmp_outfile, 'r')
local result = file:read('a')
file:close()
doc.blocks:insert(pandoc.RawBlock(FORMAT, result))
elseif mode == 'direct' then
-- @TODO write
end
:: continue ::
end
return doc
end
-- build: call the import_sources function with a temporary directory
function build(doc)
if setup.do_something == true then
system.with_temporary_directory('collection', function(tmpdir)
doc = import_sources(doc, tmpdir)
end)
return doc
end
end
--- prepare: prepare document metadata for building
-- gather, globalize and pass metadata, offprint mode
function prepare(meta)
-- check meta.imports
-- do nothing if it doesn't exist, ensure it's a list otherwise
if not meta.imports then
log('INFO', "No `imports` field in ".. PANDOC_STATE['input_files'][1]
.. ", nothing to import.")
return meta
elseif type(meta.imports) ~= 'List' then
meta.imports = pandoc.MetaList(meta.imports)
end
setup.do_something = true
-- ensure each item is a MetaMap; if not, assume it's a filename
-- nb, we change this in the doc itself, in case later filters
-- rely on this field too.
for i = 1, #meta.imports do
if type(meta.imports[i]) ~= 'table' then
meta.imports[i] = pandoc.MetaMap({
file = pandoc.MetaString(stringify(meta.imports[i]))
})
end
end
-- NOTE bear in mind some `imports` items may still lack a `file` key
-- this allows users to deactivate a source without removing its data
-- by changing `file` to `fileoff` for instance
-- check that each `file` exists. If not, issue an error message
-- and turn off the `file` key
for i = 1, #meta.imports do
if meta.imports[i].file then
filepath = stringify(meta.imports[i].file)
if filepath == '' then
meta.imports[i].file = nil -- clean up deficient values
else
-- try to open
f = io.open(filepath, 'r')
if f then
f:close()
else
log('ERROR', 'File '..filepath..' not found.')
meta.imports[i].fileoff = filepath
meta.imports[i].file = nil
end
end
end
end
-- offprint mode? if yes we reduce the imports list to that item
-- warn if we can't make sense of the `offprint-mode` field
-- if `offprints` is present we replace `collection` with it
if meta['offprint-mode'] then
local index = tonumber(stringify(meta['offprint-mode']))
if index and meta.imports[index] then
setup.offprint_mode = true
meta.imports = pandoc.MetaList({meta.imports[index]})
if meta.offprints then
meta.collection = meta.offprints
end
log('INFO', 'Offprint mode, source number ' .. tostring(index))
else
meta['offprint-mode'] = nil
log('WARNING', 'The offprint required (' .. tostring(index)
.. ") doesn't exist, ignoring offprint mode.")
end
end
--- if not offprint mode, mark the first import as `collection-first-import`
--- see below
-- build lists of metadata keys to gather, globalize and pass
if meta.collection then
for _,key in ipairs({'gather','replace', 'globalize', 'pass'}) do
if meta.collection[key] then
if type(meta.collection[key]) ~= 'List' then
meta.collection[key] = pandoc.MetaList(meta.collection[key])
end
setup[key] = pandoc.List:new()
for _,entry in ipairs(meta.collection[key]) do
setup[key]:insert(stringify(entry))
end
end
end
end
-- gather and replace main metadata using source files values
if setup.gather or setup.replace then
meta = gather_and_replace(meta)
end
-- globalize and pass the required metadata keys
if setup.globalize or setup.pass then
meta = globalize_and_pass(meta)
end
-- in non-offprint mode, mark the first import as 'collection-first-import'
-- unless this is already set to false
if not meta['offprint-mode'] and meta.imports[1] then
meta.imports[1]['child-metadata'] = meta.imports[1]['child-metadata']
or pandoc.MetaMap {}
if meta.imports[1]['child-metadata']['collection-first-import'] ~= false then
meta.imports[1]['child-metadata']['collection-first-import'] = true
end
end
-- ISOLATE
-- do we isolate sources by default?
if meta.collection and meta.collection.isolate == true then
setup.isolate = true
setup.needs_isolate_filter = true
end
-- is the filter otherwise needed to isolate some specific source
if not setup.needs_isolate_filter then
for _,item in ipairs(meta.imports) do
if item.isolate and item.isolate == true then
setup.needs_isolate_filter = true
break
end
end
end
return meta
end
--- Main filter
return {
{
Meta = function(meta)
return normalize_meta(meta)
end,
Pandoc = function(doc)
doc.meta = prepare(doc.meta)
return build(doc)
end
}
}