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|
RANDOM_SEED = math.randomseed(os.time())
MATRIX_AND = {{0,0},{0,1}}
MATRIX_OR = {{0,1},{1,1}}
HEXES = '0123456789abcdef'
local SciKGTeX = {}
SciKGTeX.whole_string = ""
SciKGTeX.properties_used = {}
SciKGTeX.property_commands = {}
SciKGTeX.mandatory_properties = {
'researchproblem',
'objective',
'method',
'result',
'conclusion'
}
SciKGTeX.PRODUCE_XMP_FILE = true
SciKGTeX.WARNING_LEVEL = 1
local XMP = {}
XMP.lines = {}
XMP.namespaces = {}
XMP.property_ns = {}
XMP.XMP_TOP = [[<x:xmpmeta xmlns:x="adobe:ns:meta/">]]
XMP.XMP_BOTTOM = [[</rdf:RDF>
</x:xmpmeta>]]
XMP.PACKET_END = [[<?xpacket end="r"?>]]
local UUID = {}
---------------------------- utilities -------------------------------
-- performs the bitwise operation specified by truth matrix on two numbers.
function BITWISE(x, y, matrix)
local z = 0
local pow = 1
while x > 0 or y > 0 do
z = z + (matrix[x%2+1][y%2+1] * pow)
pow = pow * 2
x = math.floor(x/2)
y = math.floor(y/2)
end
return z
end
function INT2HEX(x)
local s,base,pow = '',16,0
local d
while x > 0 do
d = x % base + 1
x = math.floor(x/base)
s = string.sub(HEXES, d, d)..s
end
if #s == 1 then s = "0" .. s end
return s
end
function get_output_dir()
if arg ~= nil then
for k,v in ipairs(arg) do
val, is_output_argument = v:gsub('%-%-output%-directory=(.*)','%1')
if is_output_argument > 0 then
return val
end
end
return nil
end
return nil
end
function read_header_of_file(path)
local fh = io.open(path, "rb")
if fh then
local first_line = assert(fh:read())
fh:close()
return first_line
else
print ("No xmp metadata file found!")
return nil
end
end
function extract_uuid_from_header(header)
return header:gsub('.*id=\"(.-)\".*','%1')
end
function generate_UUID()
UUID:initialize('00:0c:29:69:41:c6')
return UUID:toString()
end
function string:split(sep)
if sep == nil then
sep = "%s"
end
local t = {}
for str in self:gmatch("([^"..sep.."]+)") do
table.insert(t, str)
end
return t
end
function spaces_to_underscores(s)
return s:gsub('%s+','_')
end
function remove_environments(s)
s,c = s:gsub('\\begin%s*{.-}{.-}%s*','')
s,c = s:gsub('\\begin%s*{.-}%s*','')
s,c = s:gsub('\\end%s*{.-}%s*','')
return s
end
function remove_any_latex_command(s)
s, c = s:gsub('\\%w+%s*%[%d*%]%s*{(.*)}','%1')
if c > 0 then
return remove_latex_commands(s)
end
s, c = s:gsub('\\%w+%s*{(.*)}','%1')
if c > 0 then
return remove_latex_commands(s)
end
s, c = s:gsub('\\%w+%s*','')
if c > 0 then
return remove_latex_commands(s)
end
return s
end
function find_last_occurence(s, repls)
occurences = {}
for pattern, repl in pairs(repls) do
i, j = s:find(pattern)
if i ~= nil then
table.insert(occurences, {i,j,pattern})
end
end
table.sort(occurences, function(l, r) return l[1]>r[1] end)
if #occurences > 0 then
return occurences[1]
else
return nil
end
end
function exhaustively_replace_last_occurence_of_pattern(s, repls)
last_occurence = find_last_occurence(s, repls)
if last_occurence ~= nil then
starts, ends, pattern = table.unpack(last_occurence)
to_replace = s:sub(starts,ends)
else
return s
end
new_string = s:sub(0,starts-1) .. to_replace:gsub(pattern, repls[pattern], 1) .. s:sub(ends+1)
return exhaustively_replace_last_occurence_of_pattern(new_string, repls)
end
function remove_latex_commands(s)
replacements = {
-- contribution with * and []
['\\contribution%s*%*%s*%[%d*%]%s*{.-}{.*}%s*'] = '',
-- contribution with *
['\\contribution%s*%*%s*{.-}%s*{.*}%s*'] = '',
-- contribution with []
['\\contribution%s*%[%d*%]%s*{.-}{(.*)}'] = '%1',
-- contribution normal
['\\contribution%s*{.-}%s*{(.*)}'] = '%1',
['\\uri%s*{.-}%s*{(.*)}'] = '%1',
}
for cmd, used in pairs(SciKGTeX.property_commands) do
-- []
replacements['\\'.. cmd .. '%s*%[%d*%]%s*{(.*)}'] = '%1'
-- normal command
replacements['\\'.. cmd .. '%s*{(.*)}'] = '%1'
-- with * and []
replacements['\\'.. cmd .. '%s*%*%s*%[%d*%]%s*{.*}%s*'] = ''
-- with *
replacements['\\'.. cmd .. '%s*%*%s*{.*}%s*'] =''
end
s = remove_environments(s)
s = exhaustively_replace_last_occurence_of_pattern(s, replacements)
s = remove_any_latex_command(s)
-- remove escape chars
s = s:gsub('\\','')
return s
end
function uri_valid(s)
if s:find('http') ~= 1 then
return false
else
return true
end
end
function resolve_entity(s)
-- make sure the entity is only resolved at the innermost of nested commands.
for _, cmd in ipairs(SciKGTeX.mandatory_properties) do
if s:find('\\' .. cmd) then
return false
end
end
if s:find('\\contribution') then
return false
end
uri, found = s:gsub('.*\\uri%s*{(.-)}%s*{.*}.*', '%1')
if found == 1 then
label = s:gsub('.*\\uri%s*{.-}%s*{(.*)}.*', '%1')
entity = string.format('<rdf:Description rdf:about=\"%s\"><rdfs:label>%s</rdfs:label></rdf:Description>', uri, label)
return entity
else
uri, found = s:gsub('.*\\uri%s*{(.-)}.*', '%1')
if found == 1 then
entity = string.format('<rdf:Description rdf:about=\"%s\"></rdf:Description>', uri)
return entity
else
return false
end
end
end
---------------------------- UUID class methods -------------------------------------
-- hwaddr is a string: hexes delimited by colons. e.g.: 00:0c:29:69:41:c6
function UUID:initialize(hwaddr)
self._bytes = {
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
math.random(0, 255),
-- should come from mac address
tonumber(hwaddr:sub(1, 2), 16),
tonumber(hwaddr:sub(4, 5), 16),
tonumber(hwaddr:sub(7, 8), 16),
tonumber(hwaddr:sub(10, 11), 16),
tonumber(hwaddr:sub(13, 14), 16),
tonumber(hwaddr:sub(16, 17), 16)
}
-- set the version
self._bytes[7] = BITWISE(self._bytes[7], 0x0f, MATRIX_AND)
self._bytes[7] = BITWISE(self._bytes[7], 0x40, MATRIX_OR)
-- set the variant
self._bytes[9] = BITWISE(self._bytes[7], 0x3f, MATRIX_AND)
self._bytes[9] = BITWISE(self._bytes[7], 0x80, MATRIX_OR)
self._string = nil
end
-- lazy string creation.
function UUID:toString()
if self._string == nil then
self._string = INT2HEX(self._bytes[1])..INT2HEX(self._bytes[2])..INT2HEX(self._bytes[3])..INT2HEX(self._bytes[4]).."-"..
INT2HEX(self._bytes[5])..INT2HEX(self._bytes[6]).."-"..
INT2HEX(self._bytes[7])..INT2HEX(self._bytes[8]).."-"..
INT2HEX(self._bytes[9])..INT2HEX(self._bytes[10]).."-"..
INT2HEX(self._bytes[11])..INT2HEX(self._bytes[12])..INT2HEX(self._bytes[13])..INT2HEX(self._bytes[14])..INT2HEX(self._bytes[15])..INT2HEX(self._bytes[16])
end
return self._string
end
---------------------------- Main class methods -------------------------------
function SciKGTeX:set_warning_level(wl)
self.WARNING_LEVEL = wl
end
function SciKGTeX:warn(warning_message, ...)
if self.WARNING_LEVEL > 0 then
texio.write_nl("term and log",
[[Package SciKGTeX Warning: ]] .. string.format(warning_message, ...))
texio.write_nl("term and log","\n")
end
end
function SciKGTeX:error(warning_message, ...)
tex.error([[Package SciKGTeX Error: ]] .. string.format(warning_message, ...))
end
SciKGTeX.command_factory = {}
SciKGTeX.command_factory.cmd_top = [[\newcommand{\%s}[2][]{]]
SciKGTeX.command_factory.cmd_top_star = [[\WithSuffix\newcommand\%s*[2][]{]]
SciKGTeX.command_factory.cmd_top_override = [[\renewcommand{\%s}[2][]{]]
SciKGTeX.command_factory.cmd_top_star_override = [[\WithSuffix\renewcommand\%s*[2][]{]]
SciKGTeX.command_factory.directlua_part = [[ \directlua{
local content = "\luaescapestring{\unexpanded{#2}}"
local belongs_to_contribution = "\luaescapestring{\unexpanded{#1}}"
SciKGTeX.XMP:add_annotation(belongs_to_contribution, '%s', content, 'annotation-id')
}]]
SciKGTeX.command_factory.cmd_bottom = [[}]]
SciKGTeX.command_factory.cmd_bottom_star = [[\ignorespaces}]]
function SciKGTeX.command_factory:build_command(command_name)
full_cmd = self.cmd_top .. "\n" .. self.directlua_part .. "\n #2\n" .. self.cmd_bottom
formatted_cmd = string.format(full_cmd, command_name, command_name)
for i, line in ipairs(formatted_cmd:split("\n")) do
tex.print(line .. "%")
end
end
function SciKGTeX.command_factory:build_star_command(command_name)
full_cmd = self.cmd_top_star .. "\n" .. self.directlua_part .. "\n" .. self.cmd_bottom_star
formatted_cmd = string.format(full_cmd, command_name, command_name)
for i, line in ipairs(formatted_cmd:split("\n")) do
tex.print(line .. "%")
end
end
function SciKGTeX.command_factory:override_command(command_name)
full_cmd = self.cmd_top_override .. "\n" .. self.directlua_part .. "\n #2\n" .. self.cmd_bottom
formatted_cmd = string.format(full_cmd, command_name, command_name)
for i, line in ipairs(formatted_cmd:split("\n")) do
tex.print(line .. "%")
end
end
function SciKGTeX.command_factory:override_star_command(command_name)
full_cmd = self.cmd_top_star_override .. "\n" .. self.directlua_part .. "\n" .. self.cmd_bottom_star
formatted_cmd = string.format(full_cmd, command_name, command_name)
for i, line in ipairs(formatted_cmd:split("\n")) do
tex.print(line .. "%")
end
end
function SciKGTeX:make_new_command(new_property, namespace)
-- check if property already exists
if self.property_commands[new_property]~=nil then
self:warn([[Method newpropertycommand: Repeated definition.
Command %s already exists!
Are you sure you want to override it?]], new_property)
self:add_property(new_property, namespace)
self.command_factory:override_command(new_property, namespace)
self.command_factory:override_star_command(new_property, namespace)
else
self.property_commands[new_property] = false
self:add_property(new_property, namespace)
self.command_factory:build_command(new_property, namespace)
self.command_factory:build_star_command(new_property, namespace)
end
end
function SciKGTeX:add_property(new_property, namespace)
new_property = self.XMP:escape_xml_tags(new_property)
-- check if property already exists
if self.properties_used[new_property]~=nil then
self:warn([[Method addmetaproperty: Repeated definition.
Property %s already added!
Are you sure you want to replace it?]], new_property)
-- if not make it known to the object
else
self.properties_used[new_property] = false
end
ns_prefix = self.XMP:extract_namespace_prefix(namespace)
self.XMP.property_ns[new_property] = ns_prefix
end
function SciKGTeX:register_property(prop_type)
self.properties_used[prop_type] = true
end
function SciKGTeX:warn_unused_command()
warning_message = [[No %s annotation found!
Are you sure you don't want to mark an entity with %s?]]
for i, p in ipairs(self.mandatory_properties) do
used = self.properties_used[p]
if not used then
self:warn(warning_message, p, p);
end
end
end
function SciKGTeX:print_entity(uri, label)
if label ~= "" then
tex.print(string.format('\\href{%s}{%s}',uri , label))
else
tex.print(string.format('\\url{%s}',uri))
end
end
---------------------------- XMP class methods -------------------------------
function XMP:escape_xml_tags(s)
s = spaces_to_underscores(s)
s, i = s:gsub('[^%a%d%.-_]','')
if i > 0 then
SciKGTeX:warn([[Method escape_xml_tags: Forbidden characters.
Property %s can only contain letters, digits, underscores, hyphens and periods!
Forbidden characters removed.]], s)
end
s, i = s:gsub('^([Xx][Mm][Ll])','_%1')
if i > 0 then
SciKGTeX:warn([[Method escape_xml_tags: Forbidden characters.
Property %s can not start with xml!
Changed to _xml.]], s)
end
return s
end
function XMP:escape_xml_content(s)
s = s:gsub('&', '&')
s = s:gsub('>', '>')
return s:gsub('<', '<')
end
function XMP:add_line(...)
table.insert(self.lines, string.format(...))
end
function XMP:add_paper_node(paper_iri)
self.paper = {}
self.paper.contributions = {}
self.paper.id = paper_iri
self.paper.title = nil
self.paper.authors = {}
self.paper.researchfield = nil
end
function XMP:add_contribution(key, contribution_iri)
local contribution = {}
contribution.properties = {}
contribution.id = contribution_iri:gsub("<(default_contribution)>", "ORKG_default")
self.paper.contributions[key] = contribution
end
function XMP:extract_namespace_prefix(ns_arg)
if ns_arg == '' then
return nil
end
uri_and_prefix = ns_arg:split(',%s+?')
if #uri_and_prefix < 2 then
SciKGTeX:error([[Method addmetaproperty: No prefix found.
Unknown prefix, URI specification: %s.
Please specify the arguments as [prefix, URI]!]], ns_arg)
return nil
elseif #uri_and_prefix > 2 then
SciKGTeX:warn([[Method addmetaproperty: Too many arguments.
Too many arguments in prefix, URI specification: %s.
Excess arguments are ignored.]], ns_arg)
end
if not uri_valid(uri_and_prefix[2]) then
message = [[Method addmetaproperty: Invalid URI.
The given URI %s is not a valid choice!
Please use a resolvable URI starting with 'http'.]]
SciKGTeX:error(message, uri_and_prefix[2])
return nil
end
-- add the namespace if it has not been added yet
if self.namespaces[uri_and_prefix[1]]==nil then
self:add_namespace(uri_and_prefix[1], uri_and_prefix[2])
end
return uri_and_prefix[1]
end
function XMP:process_content(c)
c = self:escape_xml_content(c)
entity = resolve_entity(c)
if entity ~= false then
return entity
end
c = remove_latex_commands(c)
return c
end
function XMP:property_has_namespace(annotation_type)
annotation_type_t = annotation_type:split(':')
if #annotation_type_t > 1 then
annotation_type = annotation_type_t[2]
prefix = annotation_type_t[1]
else
annotation_type = annotation_type_t[1]
prefix = nil
end
return prefix, annotation_type
end
function XMP:set_title(title)
self.paper.title = title
end
function XMP:add_author(author)
table.insert(self.paper.authors, author)
end
function XMP:set_researchfield(researchfield)
self.paper.researchfield = researchfield
end
function XMP:add_annotation(contribution_ids, annotation_type, content, annotation_id)
local annotation = {}
-- check if a namespace is attached to the property specification
prefix, annotation_type = self:property_has_namespace(annotation_type)
annotation.content = content
annotation.id = annotation_id
annotation.type = self:escape_xml_tags(annotation_type)
-- take the prefix given, the prefix saved in the namespace dictionary or the default ns
annotation.prefix = prefix or self.property_ns[annotation.type] or 'orkg_property'
-- register the use of the property in text
SciKGTeX:register_property(annotation.type)
-- check if the annotation was numbered
if contribution_ids == '' then
contribution_ids = '<default_contribution>'
end
contributions_ids_t = contribution_ids:split(',%s+?')
-- add the annotations at the specified contribution
for i, contribution_id in ipairs(contributions_ids_t) do
-- add a new contribution if it has not been added yet
if self.paper.contributions[contribution_id] == nil then
self:add_contribution(contribution_id, 'contribution_'..contribution_id)
end
-- add the property annotation to the list of properties of a contribution
-- check if the same annotation already exists (in case of double evaluation of the LaTeX command for example)
already_there = false
for _, prop in pairs(self.paper.contributions[contribution_id].properties) do
if prop.content == annotation.content and prop.type == annotation.type then
already_there = true
break
end
end
if not already_there then
table.insert(self.paper.contributions[contribution_id].properties, annotation)
end
end
end
function XMP:add_namespace(abbr, uri)
self.namespaces[abbr] = uri
end
function XMP:generate_rdf_root()
ns_key_array = {}
for ns, uri in pairs(self.namespaces) do table.insert(ns_key_array, ns) end
root_string = [[<rdf:RDF ]]
table.sort(ns_key_array)
for i, key in ipairs(ns_key_array) do
root_string = root_string .. "\n xmlns:" .. key .. [[="]] .. self.namespaces[key] .. [["]]
end
root_string = root_string .. [[>]]
return root_string
end
function XMP:generate_xmp_string(lb_char)
lb_char = lb_char or "\n"
if lb_char == "r" then
lb_char = "\r"
end
output_string = ""
sorted_contributions = {}
for cb_id, contribution in pairs(XMP.paper.contributions) do
table.insert(sorted_contributions,cb_id)
end
table.sort(sorted_contributions)
self:add_line('<?xpacket begin="?" id="%s"?>',self.paper.id)
self:add_line(self.XMP_TOP)
self:add_line(self:generate_rdf_root())
--print(debug.traceback())
if self.paper then
self:add_line(
' <rdf:Description rdf:about="https://www.orkg.org/orkg/paper/%s">',
self.paper.id
)
self:add_line(' <rdf:type rdf:resource="http://orkg.org/core#Paper"/>')
if self.paper.title ~= nil then
self:add_line(
' <orkg:hasTitle>%s</orkg:hasTitle>',
self:process_content(self.paper.title)
)
end
for i, author in ipairs(self.paper.authors) do
self:add_line(
' <orkg:hasAuthor>%s</orkg:hasAuthor>',
self:process_content(author))
end
if self.paper.researchfield ~= nil then
self:add_line(
' <orkg:hasResearchField>%s</orkg:hasResearchField>',
self:process_content(self.paper.researchfield)
)
end
for i, cb_id in pairs(sorted_contributions) do
contribution = self.paper.contributions[cb_id]
self:add_line(' <orkg:hasResearchContribution>')
self:add_line(
' <orkg:ResearchContribution rdf:about="https://www.orkg.org/orkg/paper/%s">',
self.paper.id .. "/" ..contribution.id
)
for j, property in ipairs(contribution.properties) do
self:add_line(
' <%s:%s>%s</%s:%s>',
property.prefix,
property.type,
self:process_content(property.content),
property.prefix,
property.type
)
end
self:add_line(' </orkg:ResearchContribution>')
self:add_line(' </orkg:hasResearchContribution>')
end
self:add_line(' </rdf:Description>')
end
self:add_line(self.XMP_BOTTOM)
self:add_line(self.PACKET_END)
return table.concat(self.lines, lb_char)
end
function XMP:attach_metadata_pdfstream()
local xmp_string = self:generate_xmp_string()
local new_pdf = pdf.obj {
type = 'stream',
attr = '/Type/Metadata /Subtype/XML',
immediate = true,
compresslevel = 0,
string = xmp_string,
}
self.lines = {}
return new_pdf
end
function XMP:dump_metadata()
local xmp_string = self:generate_xmp_string()
local dir = get_output_dir() or '.'
f = io.open(dir .. '/' .. tex.jobname .. '.xmp_metadata.xml','w')
io.output(f)
io.write(xmp_string)
io.close(f)
end
luatexbase.add_to_callback('stop_run', function()
SciKGTeX:warn_unused_command()
if SciKGTeX.PRODUCE_XMP_FILE then
XMP:dump_metadata()
end
end, 'at_end')
-- Writing metadata packets
luatexbase.add_to_callback('finish_pdffile', function()
if XMP.paper then
local metadata_obj = XMP:attach_metadata_pdfstream()
local catalog = pdf.getcatalog() or ''
pdf.setcatalog(catalog..string.format('/Metadata %s 0 R', metadata_obj))
--if SciKGTeX.PRODUCE_XMP_FILE then
-- XMP:dump_metadata()
--end
end
end, 'finish')
-- TODO: real identifier assigned
-- get the id or generate UUID
local output_dir = get_output_dir() or '.'
local header = read_header_of_file(output_dir .. '/' .. tex.jobname .. '.xmp_metadata.xml')
if header ~= nil then
id = extract_uuid_from_header(header)
end
if id == nil then
id = generate_UUID()
print('generate new id:', id)
end
XMP:add_paper_node(id)
XMP:add_namespace("rdf","http://www.w3.org/1999/02/22-rdf-syntax-ns#")
XMP:add_namespace("rdfs","http://www.w3.org/2000/01/rdf-schema#")
XMP:add_namespace("orkg","http://orkg.org/core#")
XMP:add_namespace("orkg_property","http://orkg.org/property/")
SciKGTeX.XMP = XMP
return SciKGTeX
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