36c90af395efb0985f7f840005cb1ff9640d9d16 lrnassar Mon Jan 20 09:19:13 2025 -0800 Additional tweaks to the new docs page, more details in the ticket. Refs #30335 diff --git docs/staticPage.lua docs/staticPage.lua index f236cb7..11003e4 100644 --- docs/staticPage.lua +++ docs/staticPage.lua @@ -1,437 +1,450 @@ -- UCSC: Slightly modified to produce html that follows the genome browser -- static pages conventions -- -- -- This is a sample custom writer for pandoc. It produces output -- that is very similar to that of pandoc's HTML writer. -- There is one new feature: code blocks marked with class 'dot' -- are piped through graphviz and images are included in the HTML -- output using 'data:' URLs. -- -- Invoke with: pandoc -t staticPage.lua -- -- Character escaping local function escape(s, in_attribute) return s:gsub("[<>&\"']", function(x) if x == '<' then return '<' elseif x == '>' then return '>' elseif x == '&' then return '&' elseif x == '"' then return '"' elseif x == "'" then return ''' else return x end end) end -- Helper function to convert an attributes table into -- a string that can be put into HTML tags. local function attributes(attr) local attr_table = {} for x,y in pairs(attr) do if y and y ~= "" then table.insert(attr_table, ' ' .. x .. '="' .. escape(y,true) .. '"') end end return table.concat(attr_table) end -- Run cmd on a temporary file containing inp and return result. local function pipe(cmd, inp) local tmp = os.tmpname() local tmph = io.open(tmp, "w") tmph:write(inp) tmph:close() local outh = io.popen(cmd .. " " .. tmp,"r") local result = outh:read("*all") outh:close() os.remove(tmp) return result end -- Table to store footnotes, so they can be included at the end. local notes = {} -- Table to store headers, so they can be inserted at the end local headers = {} -- flag to see if we have to close a previous div local headerOpen = false -- Blocksep is used to separate block elements. function Blocksep() return "\n\n" end -- Print contents of `tbl`, with indentation. -- `indent` sets the initial level of indentation. function tprint (tbl, indent) if not indent then indent = 0 end for k, v in pairs(tbl) do formatting = string.rep(" ", indent) .. k .. ": " if type(v) == "table" then print(formatting) tprint(v, indent+1) elseif type(v) == 'boolean' then print(formatting .. tostring(v)) else print(formatting .. v) end end end -- remove all special chars from the string and remove all html tags function simplifyId(idStr) idStr=idStr:gsub("%b<>", "") idStr = string.lower(string.gsub(idStr, "%s+", "-")) idStr = string.lower(string.gsub(idStr, "[^a-zA-z-]", "")) return idStr end -- This function is called once for the whole document. Parameters: -- body is a string, metadata is a table, variables is a table. -- This gives you a fragment. You could use the metadata table to -- fill variables in a custom lua template. Or, pass `--template=...` -- to pandoc, and pandoc will add do the template processing as -- usual. function Doc(body, metadata, variables) local buffer = {} local function add(s) table.insert(buffer, s) end -- ucsc changes start -- debugging of meta info: -- print("vars") -- tprint(variables) -- print("meta") -- tprint(metadata) if metadata["title"] then + add("") + add("") + add("") + add("") + add("") + add("") + add("") + add("") add("

" .. metadata["title"] .. "

") else add("

No title defined in document, first line must be % mytitle

") end - add("

Contents

") for i, h in ipairs(headers) do idStr = simplifyId(h) add("
" .. h .. "
") end -- ucsc change end add(body) if #notes > 0 then add('
    ') for _,note in pairs(notes) do add(note) end add('
') end return table.concat(buffer,'\n') .. '\n' end -- The functions that follow render corresponding pandoc elements. -- s is always a string, attr is always a table of attributes, and -- items is always an array of strings (the items in a list). -- Comments indicate the types of other variables. function Str(s) return escape(s) end function Space() return " " end function SoftBreak() return "\n" end function LineBreak() return "
" end function Emph(s) return "" .. s .. "" end function Strong(s) return "" .. s .. "" end function Subscript(s) return "" .. s .. "" end function Superscript(s) return "" .. s .. "" end function SmallCaps(s) return '' .. s .. '' end function Strikeout(s) return '' .. s .. '' end function obfuscate(s) -- obfuscate the email address a la Hiram's encodeEmail.pl local refs = {} for i = 1, string.len(s) do local ascCode = string.byte(s, i) local ref = "&#" .. tostring(ascCode) table.insert(refs, ref) end return table.concat(refs, "") end function Link(s, src, tit, attr) if string.sub(src, 1, 7)=="mailto:" then src = "mailto:" .. obfuscate(string.sub(src, 7), 7) -- assume that the link label is an email address if it contains an @ character if string.match(s, "%@")~=nil then s = obfuscate(s) end else src = escape(src, true) tit = escape(tit, true) s = escape(s, true) end return "" .. s .. "" end function Image(s, src, tit, attr) return "" end -function RawInline(s) - return "" .. escape(s) .. "" -end function Code(s, attr) return "" .. escape(s) .. "" end function InlineMath(s) return "\\(" .. escape(s) .. "\\)" end function DisplayMath(s) return "\\[" .. escape(s) .. "\\]" end function SingleQuoted(s) return "‘" .. s .. "’" end function DoubleQuoted(s) return "“" .. s .. "”" end function Note(s) local num = #notes + 1 -- insert the back reference right before the final closing tag. s = string.gsub(s, '(.*)↩' .. s .. '') -- return the footnote reference, linked to the note. return '' .. num .. '' end function Span(s, attr) return "" .. s .. "" end function Cite(s, cs) local ids = {} for _,cit in ipairs(cs) do table.insert(ids, cit.citationId) end return "" .. s .. "" end function Plain(s) return s end function Para(s) return "

\n" .. s .. "\n

" end -- lev is an integer, the header level. function Header(lev, s, attr) local lines = { } if lev == 1 then idStr = simplifyId(s) table.insert(headers, s) table.insert(lines, "") table.insert(lines, "

" .. s .. "

") headerOpen = true else table.insert(lines, "" .. s .. "") end return table.concat(lines, "\n") end function BlockQuote(s) return "
\n" .. s .. "\n
" end function HorizontalRule() return "
" end function CodeBlock(s, attr) -- If code block has class 'dot', pipe the contents through dot -- and base64, and include the base64-encoded png as a data: URL. if attr.class and string.match(' ' .. attr.class .. ' ',' dot ') then local png = pipe("base64", pipe("dot -Tpng", s)) return '' -- otherwise treat as code (one could pipe through a highlighter) else return "
" .. escape(s) ..
            "
" end end function BulletList(items) local buffer = {} for _, item in pairs(items) do table.insert(buffer, "
  • " .. item .. "
    • ") end return "" end function OrderedList(items) local buffer = {} for _, item in pairs(items) do table.insert(buffer, "
  • " .. item .. "
    • ") end return "
      \n" .. table.concat(buffer, "\n") .. "\n
    " end -- Revisit association list STackValue instance. function DefinitionList(items) local buffer = {} for _,item in pairs(items) do for k, v in pairs(item) do table.insert(buffer,"
    " .. k .. "
    \n
    " .. table.concat(v,"
    \n
    ") .. "
    ") end end return "
    \n" .. table.concat(buffer, "\n") .. "\n
    " end -- Convert pandoc alignment to something HTML can use. -- align is AlignLeft, AlignRight, AlignCenter, or AlignDefault. function html_align(align) if align == 'AlignLeft' then return 'left' elseif align == 'AlignRight' then return 'right' elseif align == 'AlignCenter' then return 'center' else return 'left' end end function CaptionedImage(src, tit, caption) return '
    \n\n' .. '

    ' .. caption .. '

    \n
    ' end -- Caption is a string, aligns is an array of strings, -- widths is an array of floats, headers is an array of -- strings, rows is an array of arrays of strings. function Table(caption, aligns, widths, headers, rows) local buffer = {} local function add(s) table.insert(buffer, s) end add("") if caption ~= "" then add("") end if widths and widths[1] ~= 0 then for _, w in pairs(widths) do add('') end end local header_row = {} local empty_header = true for i, h in pairs(headers) do local align = html_align(aligns[i]) table.insert(header_row,'') empty_header = empty_header and h == "" end if empty_header then head = "" else add('') for _,h in pairs(header_row) do add(h) end add('') end local class = "even" for _, row in pairs(rows) do class = (class == "even" and "odd") or "even" add('') for i,c in pairs(row) do add('') end add('') end add('" .. escape(s) .. "" +end + function RawBlock(format, str) if format == "html" then return str else return '' end end function Div(s, attr) return "\n" .. s .. "" end -- The following code will produce runtime warnings when you haven't defined -- all of the functions you need for the custom writer, so it's useful -- to include when you're working on a writer. local meta = {} meta.__index = function(_, key) io.stderr:write(string.format("WARNING: Undefined function '%s'\n",key)) return function() return "" end end setmetatable(_G, meta)
    " .. caption .. "
    ' .. h .. '
    ' .. c .. '